Of the new wave of Marvel/DC movies, of the ones I've watched so far, my favourites were:
Spiderman 2
Superman Returns (also because I'm a bit of a Kevin Spacey fanboy)
X-men 2
and the ones I really disliked were:
Batman Begins (that movie has zero congeniality, and ultimately pales in the face of Burton's approach to the matter)
Fantastic Four (the first and only time I went wtf out loud afterwards in the theater)
X-men 3 (I know next to nothing about the x-men universe, so the sacrilege factor falls away, but it was just poor plot, tons of logic mistakes and overdone claptrap)