First, the ideal lift will depend on use case. If this is a road vehicle that you just want to look and feel a little more "jeepy", then ride quality is king. If it's going to be towing a small boat or pop-up or something for you, you'll want a little stiffer rear end to account for that. If it's going to be trail ridden, then you can afford some components that don't ride quite as well in favor of putting the additional expense towards some basic armor. Even a basic gas tank and TC skid combo will significantly improve the trail survivability of an XJ. There's also different choices to be made as far as maximizing flex within a given lift height. A lower lift pack plus shackle relocation and longer shackles can increase flex over a simple lift pack for example. Looks also come into it, what size tire do you want to run? Do you mind fender trimming? We can help you better if we know what you want to do.
Second, be prepared for a LOT of maintenance costs. Lifts stress maintenance parts and all sorts of other things and even at 3" the costs pretty much always snowball between highlighted maintenance parts, tires and minor modifications that get overlooked (more below). Now for the details.
There's a few different ways to lift the rear we can discuss:
1) Shackle lift: This uses a longer shackle to push the body up from the leaf spring. On worn leaf packs, this causes increased stresses and can actually result in flattening the back half of the leaf spring as much as lifting the body off of it. That bend out of shape adds extra stress and can cause leaves to crack or break entirely. I only suggest a shackle lift in conjunction with brand new leaf packs (either stock height or lifted).
2) Short AAL: This places a very stiff, short leaf into the pack. The arch and stiffness of that leaf allow it to force the entire leaf pack into more of an arch, lifting the body of the vehicle further off the ground. Since that leaf has to be SO stiff to arch the whole pack with poor leverage, it really hurts ride. Short AAL's also create stress points for the rest of the pack at the ends of the new leafwhich can definitely cause cracking or breakage over the long-term. The additional arch also shortens the eye-to-eye length of the stock main leaf, that can pull your shackles vertical, which limits your flex and hurts ride beyond just the characteristics of the spring itself. . That can be combated with shackle relocation. Short AAL's are not recommended unless budget allows nothing else.
3) Long AAL: Long AAL's work just like a short AAL, except that they are nearly the full length of the stock main leaf. This puts them higher in the pack, allows them to be a little softer due to greater area and leverage and generally make for a better ride and more flexibility than a stiffer short AAL. They do suffer from the same problem of shortening the eye-to-eye length and hurting flex/ride if they pull your shackles too vertical. That can be combated with shackle relocation. They're acceptable in general as a budget option. Bastard packs (using leaves from a junkyard vehicle to add more arch to your factory pack) have similar characteristics to Long AAL's. S10's and XJ's are most commonly used to supplement the factory XJ packs, though any 2.5" wide leaf will work if you cut it to appropriate length. Bastard pack options
4) Lift packs: Lift packs are a whole new leaf pack specifically designed by the aftermarket to lift an XJ a certain amount. They don't suffer from the additional stress problems of AAL's or shackle lifts, and the ride tends to be better due to an internally complimentary spring rate from each leaf. Assuming you don't get the wrong sort, they also don't suffer from the Eye-to-eye length problem. Putting 'HD' packs designed for heavy tire-carrier bumpers or towing can result in their not being enough weight on your rear end to properly compress the spring, bringing up the eye-to-eye issue in absence of a shackle relocation to let you dial in the angle.
Technically there's also blocks but it's a REALLY bad idea on XJ's due to the relatively thin, narrow, weak leaves. Just, don't do it. Period. At most I could only endorse a 1" or less block used purely for leveling purposes.
So...my suggestion for 3"? If you can afford it, get 3" lift packs OR 1.5" lift packs (crown or dorman HD leaves, they mimic the towing/upcountry package factory leaves) and a bolt-in shackle relocation like IRO or RC's (one of the few RC products I'll ever recommend). The latter allows you to use a longer shackle and likely has the greatest flex easily available at 3". It also allows you to dial in shackle angle and helps with ride. If you can't afford new leaves and have to do an AAL, make sure it's a long leaf or a thought-out bastard pack if possible. At 4.5", you'd similarly want 3" lift leaves and shackle relocation. If you need to cut costs, use a full S10 pack under your XJ main leaf to net a 3" lift pack that'll work with relocation to give you 4.5"ish overall.
For the front suspension it's just a matter of getting good coils and/or spacers in a height you like (there are other concerns for the vehicle discussed below). At 3", look around for a well-reviewed kit or coil. Plenty of options. I personally really want MetalCloak's 3.5" springs, or perhaps the Moog Variable rate coils (which lift 1-1.5" depending on things like aftermarket bumpers) + a 1.5-2" spacer. The variable rate coils have excellent reviews for road manners and, due to their design, can be capable of more droop than a similar length single-rate coil. If you want to get advanced, you can talk spring rates. Stock (non-upcountry) XJ springs are, i think, 160 in-lbs. V8 ZJ are 180. 180 +/- 10 is pretty common in aftermarket springs. Stiffer springs will compress less, which makes them more dependable for heavy winch bumpers and the like and also help control body roll. Softer springs will compress more, making ride height more strongly affected by accessories. Softer springs are also more prone to body roll and lateral flex, ESPECIALLY at speed. However, a longer soft spring that is much compressed has more droop/downtravel available than a stiffer, shorter spring. So softer springs are, in some ways, very much preferred for dedicated trail rigs, which stiffer ones are needed for on-road vehicles to help control the additional flexion and keep the vehicle safe during turns, especially on the highway. That has a lot to do with why some guys claim a sway bar is silly (they have stiff springs) and others claim they felt like they'd die the first time the drove without it (softer springs, more roll). Guide to aftermarket springs options and rates
. At 3" though, most of that is pretty much a wash other than your personal perception of ride quality, which will be more affected by shock choice. Just get a 3" coil from a reputable brand and be aware that with a stock bumper you may not have enough weight up front to really compress it and you may wind up with more like a 3.5-4" lift. Read reviews before buying a kit to confirm that sort of thing. LOTS of lifted XJ's out there. Someone has probably tried it.
Now for the miscellaneous considerations at 3"
1) The track bar: XJ's use a bar that mounts to the driver's side of the frame and the front axle to keep the axle centered. When you lift, the angle on that bar increases and its effective width decreases. That pulls the axle left, out of center. You can address it by drilling a new hole on the axle farther to the driver's side, but the metal is soft and prone to wallowing out over time. The "right" way to do it is to purchase an adjustable track bar from a vendor like rubicon express, IRO, RC, etc.... Those bars have a changeable length, like a tie rod. you can dial it in to keep your axle centered, and adjust it later if your lift sags, you go higher, or whatever other reason.
2) Brake lines: 3" of lift is kind of pushing the factory brake lines on-road. If it's going off-pavement, they NEED to be replaced. There's no need to blow a lot of money on aftermarket braided steel lines though. Simply get a set of YJ soft lines for the front, and a YJ or Dakota rear line. They're built to the same quality as a factory replacement for your XJ and the pop right on with no modifications. They're just designed for a vehicle with more distance from line mount to axle so they have enough length to accommodate your lift.
3) Driveline angles. At 3" your 94 may not experience any issues, but if you lift and then experience vibrations/growling sounds, it's likely because lifting the jeep changes the angles experienced by your driveline. The rear is the most sensitive. The cheap solution is to drop your transfer case a little bit. That involves removing the transmission cross member and its factory bolts, then reinstalling it with longer bolts and spacers between the crossmember and the body. Easily done for ~$15 at a hardware store. That does reduce your ground clearance however. The 'right' way to do it is an SYE, which moves the the flex in driveshaft length to the shaft, rather than the yoke, and allows you to use a different sort of driveshaft called a double cardan shaft. Look at your front driveshaft and how it connects to the transfer case, that's what the rear would look like after an SYE. In fact if you don't get a "short" SYE, you can use an XJ front shaft from a donor as part of the SYE install to significantly reduce costs compared to having a custom shaft made. Drivelines 101
4) Sway bar links: Your factory sway bar links will not be long enough to maintain a good sway bar angle at 3", and may cause the bar and your coil springs to interfere. Some lifts come with extended sway bar links. Some, like RC lifts, come with relocation brackets that drop the bar itself down and forward. I don't recommend those, it leaves your sway bar out and exposed. If neither or you want to replace drop brackets, an easy, cheap solution is to use TJ sway bar links. They bolt right up and are about 2.5" longer than stock XJ links. Great for a 3" lift. For longer links on a budget, WJ links can have a U bracket added to the top and be used. They can also serve as the basis for homebrew quick disconnects. There's also plenty of options for home-brew or aftermarket "quick disconnect" links, which I recommend if this is going to spend a lot of time swapping between on- and off- road duty but aren't really helpful if this is primarily a road vehicle. My favorite homebrew disconnects
5) Control arms: Control arms cause a lot of discussion. You can generally get away with stock length arms at 3", though it can result in rubbing where longer ones wouldn't. The point of different length and adjustable control arms is to keep the axle and the driveline at good angles. As you lift, you angle the front of the axle down, resulting in your knuckles turning pointed at the ground instead of parallel to it and causing binding (thus vibes and wear) in your front driveline. Longer Lower LCA's have much the same effect on front driveline angles that shimming can on rear, and can resolve pinion/knuckle angle problems that might otherwise arise. A full set of adjustable arms allows greater control over the forward/rear positioning of the axle in the wheel well and full control over the pinion angle. Basically, if you pick up fixed LCA's as part of the lift kit, like RC sells, then you should use them. If you're buying them separately, you should ONLY bother with adjustables, with priority given longer lower arms. You may also hear mention of long arms, or control arm brackets. Both of these are really only of interest at 4"+ in height and make the arms flatter at neutral ride height height. This improves ride by making the front axle more responsive to bumps (the steeper angle of factory location control arms on lifted jeeps makes more of a bump transfer straight into the unibody, and less of it to the suspension). They also allow more flex, because factory arms are already at a significant part of their droop potentional at neutral height, and longer arms only fix so much of that since they're still at an extreme angle. . Short version: if the kit comes with fixed arms, use them. If not, don't worry about it unless you have problems up front. IF you do, get adjust lowers, if not lowers and uppers, and either google "XJ driveway alignment" or have an offroad specialist shop set it up for you until you're more comfortable.
6) Maintenance parts: When you lift, ANY worn part in the suspension or steering will be highlighted. Balljoints, TRE's, wheel hubs/bearings, driveshaft U-joints. All of those sorts of things are going to complain quickly after being lifted if they're not fairly new. I should also mention here that replacing the control arm bushings up front (whether you get new control arms or not) will really help reduces noise and ride harshness. Sway bar bushings, too. I STRONGLY recommend checking out Rockauto.com or SummitRacing.com. For high-quality steering parts (accept only Dana/spicer or Moog's Problem Solver line. Oh and Timken for hubs) I have not seen anything short of ebay which can match their prices. ~60% the cost of Moog PS stuff at Oreilly's for example.
A final piece of advice: XJ cooling systems are the most commonly ignored and most temperamental of an XJ's regular maintenance systems. Rockauto or Napa (due to who makes their store-branded parts) are the best place to get replacements. If it's all original, or has been several years, I would consider it good sense to do thermostat, radiator hoses, fan clutch and water pump this coming spring. You should do a system flush while you're in there.
There's plenty of brands to look at, I recommend you search this forum and online for reviews. Zone is the one that's better received and almost identical in price to the Rough Country 3", but Rubicon Express, Rusty's, Metal Cloak, IRO, Rusty's, Pro Comp, OME and Rugged Ridge are all examples of good lift companies. You can also assemble your own from your favorite components/features. That's more complicated and can be more expensive, but makes the rig truly built to spec for you.
Let us know if you have questions on any part of that. I know it was a huge block of text but hopefully it helps you understand what you're getting into and what you're comparing as far as the types/completeness of the lift kits your looking at.