Comic Zeal is currently the best app for reading comics on your iPad. Whether you're a member of the mighty Marvel marauders, a dedicated DC-for-lifer, or someone who prefers the alternative and independent sequential art scene, if you already have your comics in a digital format -- especially if you bought those massive Marvel DVDs containing all the early issues of Avengers, Fantastic Four, Spider-Man, X-Men, etc. in PDF -- Comic Zeal should be your go-to reader.
You can sync PDF, CBR/RAR, or CBZ/ZIP files straight over to Comic Zeal from iTunes via file sharing if you absolutely have to, and with Wi-Fi sync it's easier than ever. I just drop mine into Dropbox, hit the Dropbox app on iPad, download them, hit the action button, and tell Dropbox to open them in Comic Zeal. It would be nice if Comic Zeal could hook into Dropbox (and other online storage pools) directly, eliminating a step. Here's hoping we get that in the future.
Comic Zeal also has a lot of great options for organizing and displaying your comics, including by series and in a grid, so you can more easily find the issue you want, when you want. You can choose between swiping or tapping -- or both -- to change pages, tapping or hitting a button -- or both -- to show and hide the navigation tools, and a variety of other features, including zoom. Alas, you there's no tactile way to manipulate your comics (you can't put them into "jiggly mode to re-arrange or delete them, or put them into folders), and turning pages lacks the iBooks-style animation and doesn't feel as crisp as it ought to.
If you already have comics in a digital format, Comic Zeal is simply the best way to read them on your iPad.