Damn, you guys already listed most of the best ones. Well, feeding the fire -
1) Love interest cliche: yeah, very hard to pull off.
2) Leather: bleh. Everyone knows leather only looks good on women, and even then...
3) Side-character insists central character has a heart of gold: see 2004 Punisher. One of the drawbacks of this film would be that the film wants us to believe that the Punisher has a heart of gold underneath it all when part of the idea of his character is that he doesn't really have one, or at least not much of a heart left.
4) Too many "make a choice" speeches directed at the superhero by his supporting cast or random side characters.
5) The villain upstages the hero.
6) People who are generally good actors are cast to play heroes/villains whom they physically do not match (diminuitive Michael Keaton as the normally hulking Batman, towering Hugh Jackman as the traditionally short statured Wolverine, stringbean Topher Grace as the normally muscle-bound Venom).
7) Casting young unknown actors to play superheroes and claiming you're doing it for the benefit of the audience when in reality you're just hiring lesser known actors because it's cheaper.
8) Briefly highlighting the villain as a mentor to the hero.
9) Inconsistent tone, wildly going back & forth between dead serious and camply self-mocking humor (the Krypton/Jor-El/Superman at work moments VS the goofy Lex Luthor moments in the 1978-1987 Superman series; Daredevil's crime-fighting contrasted against the fact that his clients are so poor they can't pay him properly).
10) Fight sequences that make no sense (Matt Murdock VS. Elektra on the playground).
11) Pointless costume change from book to film (c'mon guys, if Richard Donner didn't screw with Superman's costume, you guys don't have to screw over the costumes of other characters!). Not sure if that's a cliche or not, so it's open for debate.