PDF Expert 5 and its companion Documents (use it as the main document reader/editor; syncs with cloud services and svn; annotating PDF in a sophisticated and elegant way)
LiquidText Annotate & Excerpt PDF documents in a flexible way
Pocket (Read It Later) (to accumulate readings while offline or commuting or…; iPad/iPhone/Mac in sync)
Newsify (the best RSS Reader Client; iPad/iPhone/Mac in sync)
Google Chrome browser (alternative browser to access sites in desktop format; iPad/iPhone/Mac in sync)
Pressreader (read newspapers and magazines using the UniBZ Library subscription)
Air Sketch (turn your iPad into a wireless whiteboard and PDF annotator: anybody with a HTML5 browser in the local network can follow the presentation)
Doceri Remote (turn your iPad into a controller of your mac/windows desktop - connected to a projector - superimposing a whiteboard with a pointer)
AirServer (An AirPlay receiver for Mac and Windows: can stream content or mirror the display from an iPad/iPhone/Mac)
Air Display (turns your iPad into a wireless display, to extend the mac/windows screen)
eBanner Pro (scrolling banner application; it displays your messages like LED dot matrix board - for iPad and iPhone)
Classroom
TeacherPal (enables the teacher to organize classes, to track the attendance, grades and behavior of students) (I'm not using it)
Draw
iDraw (the most feature-packed vector drawing app; also with a Mac app)