"If it looks useful, slap it on the ship!" That, and reliability. I try to maximize travelled worlds over limited playing time, so fewer launches and fewer burns are better. No mods except Alarm Clock (yet). My go-everywhere ship (I only use one type for everything) has a rover, all the science stuff, a Kerbin-return capable lander, a manoevring orbital refuelling station also carrying four Kerbin-return capable "escape pods", and extra docking ports just in case. If something goes wrong, as it always does, this ship is the perfect self-rescueing princess. (Unless it happens planetside - maybe I should add a second lander... You can never overengineer enough! ;-)