Interior: OK, if you wheel in mud--again, we don't mean just a mud nut or even people who wheel in 2-foot puddles--at some point, your interior will take a beating. Unless you are in a TJ or JK with a hardtop, never go past the line where the top meets the body, and never get out of it when you get stuck; you'll get water, mud, and/or guppies in your Jeep. The sooner you accept that, the less stress you'll have in your life.
Carpet will trap water and mud, leading to rust. Pull it out and put some kind of spray-in bedliner down. No matter what you do about the carpet and low-hanging interior components, there are two things to check out: electric-component water-resistance and location of electronic components. Make sure your switches can handle the occasional dousing. Mount your radio, CB, and cappuccino machine as high as possible. Tuffy's overhead console is a nice non-fab-needed solution.
A good rule of thumb is the body line between the top and the tub. If you run in the wet stuff, anything under that body line will, at the very least, get an occasional dousing. Don't mount your amplifiers to the floor. Don't put your CB on the hump in front of your shifter. Don't put your light switches on the console near your hands. Mount things high, and if you are in doubt, cover the connections in liquid electrical tape, and make sure it is fused.
An ounce of prevention is worth a pound of cure. If you buy a used Jeep, look at every electric thing in the interior and make sure it's got a rubber boot or something to shield it from the elements. Plan for the worst with everything you add, and mount the parts accordingly.
Tires: Run mud tires. The bigger the voids, the better they'll be when the going gets gooey. Avoid directional tires; they're usually really good at getting into trouble but really bad about getting out in Reverse. If you're already saddled with directional tires, try running some or all of them in Reverse and see how that works for your application.
Suspension: Run whatever lift you need to in order to clear the tires you want. Cut where you have to, but remember the Jeep frame is the best anchor you'll ever see. Second to that are your front and rear axles, so run the biggest tires you can with enough lift to make them fit without going crazy tall.
If you're driving a leaf-spring Jeep, consider a shackle reversal a necessity. Just make sure your driveshaft has enough slip to handle it. We've ripped quite a few frame-mounted spring perches off Jeeps that still had the shackle on the front of the spring, not to mention the bent springs from hitting that wall hidden deep in the muck. A shackle reversal will help immensely with bent and broken leaf-spring parts up front.
If you're running a coil-spring Jeep, ditch the stock tinfoil control arms and track bar, even if you have a short-arm kit. It's the same principle here as with the shackle reversal--beefier parts will stay under the Jeep when you hit that unseen wall in the mire.
Steering: Run some kind of steering-box brace. If you're upgrading the tie rod and drag link, steer clear of rod ends or heim joints--they just don't handle mud and wetness well (not to mention being illegal in many states for a road-driven Jeep). Go with bigger tie-rod ends and either ream the knuckles to accept the new taper or get bigger custom ends with the stock Jeep taper.