Utilities Folder: contains important utilities such as Bloomberg (stocks), DropBox, Pastebot, Find my iPhone, and Sleep Cycle (my alarm clock).
Calcbot: My preferred iteration of the calculator for the iPhone. It saves your calculation history and has a gorgeous UI.
Apple Folder: contains most of the built in apps (iTunes, Clock, Notes, Compass) that I don't use as often as the ones that are not in that folder.
Things: A great task manager that I use to organize my HW, and other random tasks. It syncs with a version for my Mac and iPad.
Reeder: My favorite RSS reader. Syncs with Google reader, and also has an iPad version which has a stunning UI.
Rdio: A subscription music service I am trying out.
Dock: Default [Phone - Mail - Safari - iPod] setup that iPhones ship with.