I don't care for AU, to be honest, but there are a few I like.
I happily second
maddoggirl's self-rec for
Bloodlines, featuring House and Wilson as soldiers in the Civil War. A really excellent story.
nightdog's
Annals is wonderful and I hope we'll get more one day (hint hint).
Letters of Transit offers a fascinating glimpse into an AU world too.
No Little Charity by
perspi is wonderful. All three are House-Wilson friendship.
kohl_rimmed_eye, also called
paperclipbitch, is an extraordinary writer who writes Wilson/Chase slash. I don't like that pairing particularly but her stuff is just so good I read it anyway.
Grey Gardens is an AU where Wilson had the infarction; very angsty but ends on a happier note. Its sequel
April Fools is the story of AU Wilson's life. Those squeamish about slash can just skip the last few paragraphs.
This may not be what you're looking for, but our lovely pwcorgigirl's
The Past Is Another Country looks at five different ways House's life could have turned out.