I have been using a multi-platform Quran browser called Zekr (zekr.org) for reading the Quran on my computer. I still use online Quran browsers for research as well, like TIM, but having one I can use offline is useful for me. I imported both the Progessive Muslim (The Message) and Khalifa's translations and can view them side-by-side with the fully vocalized Arabic text (if someone wants the translation files to import into zekr, email me). It's highly configurable, and you can create bookmarks, listen to recitations, and it has a pretty good search function, but unfortunately it only searches the Arabic text.
Besides online sources and, of course, hardcopy books, what other Quran programs do people use for study?
-l