Can I answer the Top/Bottom question as an obsessed H/W!porn reader? This is actually a fascinating topic for me, and consequentially, the theme of much fanwank. You've bee warned.
The whole issue for me is about different kinds of power. House as a top and Wilson as a bottom feels right to me, because those roles seems to be the extension of their relationship on screen, sex as a symbolic(ating- what?) but also completing act to everyday life. Now, I don't mean the House being dominant and Wilson being a doormat concept, it goes deeper than that (teehee). From House's end - his jealousy and possessiveness towards Wilson, wanting to claim him completely, to own him. For House that would translate as fucking him. In Wilson, first of all there's the passive approval he gives House to intervene in his love life (he never really draws a line, never says "back off, it's not your damn business") Secondly there's his constant caring and worrying for House's sake, his lectures and demands and manipulations. It seems Wilson would want to be able to control House's actions entirely. Now this is trickier, but for me that translates into wanting to consume House ---> have House in him, as well as to be taken by him (passively agreeing to House's possessiveness).
For some reason there's a notion going around that top=better (probably because it's, traditionally, the male's job). There is so much strength in receiving, in consuming, in submitting. A strength that, to me, House doesn't sustain and doesn't really get. But Wilson does.
This fic depicts my views so much better than I just did. (it's also my favorite for a long time now). 4 parts, NC-17 with BDSM themes (naturally :P)
House as a bottom and Wilson as a top is usually OOC for me, because as I've said, I see a lot of psychological meaning behind those roles and it clashes with the way I grasp the characters. The only time it felt right for me that I can remember, it was non-con. But I'm guessing that the right writer work it.
TL;DR?