Well, I use (almost everytime) two "Dawn", or even better, a "Weir" from Phoenix Industries Mod, coupled with a KAL-1000, a kOS processor, a command pod, a Xenon tank and some legs. I know it isn't very legit, but it works and it's not even a mod (I mean, for the effect, not the "Weir"). That's a stock feature of KSP.
Well, I use the robotic Hinges and Pistons (from stock KSP) and the straight rails (from JxFab Utility System) to maximize the room in my spaceplanes, I do something like this: I use robotics to move the upper Mk2 parts in the direction of the arrow. Then I have access to plenty of hidden stuff, on the blue sides. Also, the huge wheels are quite useful when you need to move enormous ships or spaceplanes, like the ones in the OPT spaceplane mod.
The aero parts allow you to build boxes and big structures, and moar wings, when the big jets are for Laythe or Kerbin Airlines, e.g. for a stratolauncher which uses jets to reach 15 km.
The place-anywhere RCS port can be used to provide an impulse, like when you go to Gilly without puffs nor LF or OX.
The material bays are quite useful for middle-game science storage, before you get the fabled Mk1 + Mk2 + Robotics I mentioned.
The terrier/poddle/dawn are nice in early- and middle-game, and when you need small engines for your base or interplanetary travel with high TwR.
And for the stayputnik and the LES, well… You can try to go to Minmus with that, but dont bet on it .