Filesystem apps come to mind especially.
Zen Viewer
iFiles
GoodReader
DownloadsHD
ReaddleDocs
For some reason some folks have been saying the iPad has no filesystem. It does, in fact, have plenty. Lots of options, all downloadable, and a few of them are quite feature-rich.
Beyond these, the apps that have more than made my iPad purchase worth it:
iCab
Azul media player
Evernote
Notability
Penultimate
Reeder
Feedly
Pages (WriteRoom is a gem for word processing as well)
GoodReader
DropBox
iTeleport (VNC on the iPad is amazing)
And of course, Air Video