Spider-Man 2 and Spider-Man 2.1 are essentially the same movie. I don't really value one over the other. I like them better than either version of Superman II, which unfortunately was hurt by behind the scenes problems. Even then, I suspect I would pick Spidey just because I like that movie so much. I also prefer it to the first Superman.
Between the Superman IIs, I prefer the Donner Cut. It cut out some of the goofiness and even though the role is small, I thought Jor-El being in the film added a lot to the emotional punch of the film and he was sorely, sorely missed in the Theatrical Cut. That final scene between Clark and Jor-El is at the heart of the entire film and it simply wasn't there at all in the theatrical version. I also much preferred the Donner version of the scene where Clark finally admits to Lois that he's Superman, another key scene of the film. And that one was just patched together from screentest footage!