Personally, I'm a big fan of Kenwood's Excelon line. I have the KDC-X993 and love it! It has bluetooth, and I ran the usb/aux inputs into the glovebox to keep them out of the way. I personally don't use iphones or ipods, so I chose to use thumbdrives to store my music which I just plug in inside the glovebox. They're out of the way, and low risk of being stolen--and most importantly for Jeep owners, shock proof unlike cd's. It's a bump ride in my Jeep, and I don't have to worry about skipping, buffering, etc.
Pioneer and Alpine both make great products too, but I'm partial to Kenwood's headunits.
'99 TJ Sport | Rampage Frameless | 33x12.50x15 Goodyear MTR/K's | Poweraid TBS | Flowmaster 40 series | Herculined | 15% tint | LED interior lighting | AtoZ front/rear bumper | AtoZ tube rocker guards | Kenwood Excelon KDC-X993BT | Kicker 6.5's in soundbar | Alpine Type-R 4x6's in dash.