A few notes: Ruby Rhod was supposed to be annoying. A self-important, high-speed diva personality put into a small-scale war situation, is it any wonder the dude was screaming his head off? Most civilians in general would have at least comparable reactions to suddenly being shot at, nearly blown up and then given responsibility for activating a portion of a device to stop the end of the world...
Joffrey was Joffrey and not at all likeable, hence why he was who he was.
Carrey's Riddler was over the top, and yeah very much a departure from the previous two films' tones, but I personally see Forever and the sequel as more Silver Age Batman than Dark Knight era Batman... so it wasn't bad from that perspective. Hell IIRC the Adam West versions were comparable in terms of over-the-top antics. However, I feel had they gone more Dark Knight with that film, I think Jim Carrey has the range to pull off a more serious Riddler, he just gets pigeonholed into comedy characters because of his career.
Samwise, no... not really annoying but I do feel the way Fellowship and most of Two Towers followed the books so close (with a few liberties taken with characters like Arwen and other important characters) that when Jackson decided to hugely depart from the end of Two Towers and all was more annoying than any character in those movies could be. Samwise was pretty much the character from the books though and in my view that couldn't be annoying at all.