While I get that there's a pecking order even among nerds, I'm frequently put off by how badly the main characters treat Stuart, the comic shop owner.
Not really. Steve Urkel was a nerd, but in the show that just meant “annoying personality”. The characters in Big Bang Theory might have annoying personalities at times, but at least had interests and attitudes that demonstrated they were actually nerds, not just annoying.
It would be like if someone said they liked “movies”, but never mentioned a single movie that they enjoyed, or actor, or director, or anything. Just they’re really into “movies”.
Big Bang Theory has many flaws, but it is so far better than Steve Urkel or Screech. If I had been a kid when Big Bang Theory came out, having some positive nerd representation would have been wonderful. And in Big Bang Theory the characters are represented positively—the show clearly likes the characters, to use Roger Ebert’s terminology.
It genuinely made me uncomfortable; not because I like Windows 8, mind you. It was just so uncanny and out of place.