On my old XJ, the exhaust pipe runs VERY close over the top of the trans/xfer case crossmember. If the engine is running the least-bit rough, it shakes a bit ...enough to cause the pipe to make slight contact with the crossmember, causing a "shaking sound" very much like the OP describes. You can't really pinpoint where it's coming from when inside the Jeep, because it resonates through the whole bottom side.
After the engine got about 175k miles on it, no matter how much I tried to smooth the idle out with a tune-up, it would still do it sometimes (i.e. cold mornings, etc.). I finally jacked it up and gained enough clearance by reefing on the pipe with a large bar.
Just something cheap to check (clearances of exhaust pipe to frame members etc.)