Marvel and DC Comics
Big time publishers like Marvel and DC both offer free comic book apps on iTunes, and they serve as a front-end for the publisher's online comic book store. Even if you don't plan to spend any money, it's worth downloading the apps because they offer freebies from time to time.
Probably the first one many people will go for is the Marvel Comics app because it includes titles from the likes of The X-Men, Spider-man, The Avengers, and so on. Although I do not subscribe to Marvel's online comic service, I understand that their web-based service is not compatible with this one through iTunes, so you can't exchange libraries. This seems to be a major point of contention based on some user reviews seen on iTunes.
The DC Comics app interface is basically the same as Marvel and they offer anything you can think of from the DC library, such as big names like Superman and Batman, and even a free first issue from a World of Warcraft series. They also have a bunch of origin type comics available for free, such as those for Wonder Woman, Lex Luthor, Green Lantern, and more.