Notational Velocity is a cool way to keep textual notes.
I always had issue of manually deleting the archive after extraction, Unarchiver helps with that.
Want to have your favorite websites into Mac desktop applications, use fluidinfo.
Almost every one fiddles with different To-Do list management tools.
I find Skim more useful than Adobe PDF reader as it also serves the purpose of note taking and is a useful aid, if you plan a more disciplined study.
If you are not satisfied with Google Reader then Gruml will allow you to view and manage your feed subscriptions of your Google Reader account on Mac OS X.
I have a pencent to use different browsers apart from Chrome and Firefox, just for fun. Some of the notable ones are Camino, Opera and a useful web automation tool called Fake!
Adium is a good replacement for iChat on Mac OS X
If you want a image viewer that would run through a folder without having to select the image like you need to do with preview application, you could use cocoViewX :