DiskAid - $9.99 (Not an iPad app but allows you to browse and copy iPad files from your Mac)
Stanza Free - (wish it were still supported) - can't beat it color options for night reading and other preferred settings. Also adjust brightness by a simple up or down swipe.
SurgarSync instead of DropBox as you can select ANY folder to be an "update folder" - If you want to try it there is a free 5 gig account available (see small text link under the big paid "plans" shown at the top of their page.)