I do a slow (evil) negative on the last set of all my 5X5's (and just about any set of anything, last rep) and it really seems to make a difference. More DOMS the next day. More gains overall IMHO.
I know guys who do lots of reps with negs, and I don't see any substantial difference between them and other "regular" programs such as 5X5, pyramids, straight sets, etc. I think the program itself works first and the negs are suplemental/beneficial to it.
But I'm as full of shit as the next guy so take it for what it's worth.