The one nit I've always had is whether third-party apps/sites link the @ symbol when attached to usernames. I prefer unlinked @ symbols (as seen on twitter.com site), but even so, search.twitter.com links the @ symbol... how consistent.
search.twitter.com is still a separate app all-together (purchased from I-don't-remember-whom). Twitter officially intends to roll it into the rest of their internal apps and API at some point. You're right, it is inconsistent, but at least there is some sort of excuse.
Well yes, I know. They acquired Summize well over a year ago, and it would probably be a one-line code change. It's probably not a high priority issue for them, but it still bothers me :)