As a stand-alone film, I think X-Men: The Last Stand, is pretty weak, but as a third act to a story, it's very good, because it doesn't focus on character (which is set up in the first two acts) and has many things from the franchise pay off throughout its running time.
I'm not a comic book fan, so I don't know the origins to these characters, but I just grade them in entertainment value, not faithfulness.
Anyway, here's my Top Ten List (and it can have as many movies from one series, unlike the MSN one):
10. Daredevil - I liked it.
9. Hellboy
8. Superman Returns
7. The Incredibles
6. X-Men
5. Batman Begins
4. Superman II
3. Sin City - Marv's a superhero
2. Batman Returns
1. X2: X-Men United