Red

Air up the tires, rinse of at least the underbody if possible. Do the checks that you would at a filling station - oil, coolant, etc. Check for loose, broken, dented, bent, or otherwise damaged parts. Drive slowly at first, paying attention to all the systems. If something doesn't seem right, stop and check it out.

OnBelay

X 2 on Toad's post. After washing everthing, I re-torque the control arms and steering linkage. It's amazing how some of the bolts can come loose. Heck, once I even had a bolt shake loose and land in my LAP while offroading! It came from up by the sun visor.

j33per

If you've been through water, I'd check for water contamination of the oil in my diffs... On the JK it's really easy to get the oil out of the diffs. If the oiul looks "milky" replace it with new oil (80w90) and if not contaminated, simply put it back in...