I haven't seen Ghostbusters II since I was a kid, and while I remember not liking it as much as the first, I can't remember what there was about it that inspired the hatred it gets on the web. So I'll (cautiously) call that underrated.

I think all of the Indiana Jones sequels (prequel if that's what you consider TOD) are underrated.

The first three Die Hard sequels are all underrated to some extent.

Star Trek III

Spider-man 3 and X-Men: The Last Stand are not as worthless as some would have you believe.

The Matrix sequels do not rank as two of the worst films of all time.

Terminator 3 and Salvation have a number of redeeming qualities.

The Star Wars prequels are much better than their reputation suggests (especially ROTS).