(I'm a professor in the humanities.) Aside from obvious, MS Office, and Endnote, I find the following very useful:
For WRITING:
Scrivener from Literature and Latte: this is a writing project organizer of sorts. It makes juggling long writing projects much easier and provides a way to keep notes in lots of different files that are actually very accessible. Before Scrivener I'd have dozens and dozens of word files stuck in folders all over the place.
MacJournal from Mariner Software: this is also a way to keep lots of different files within the same interface, but it works very well for keeping notes on different things. For planning classes this is particularly useful for me as I start a journal with that topic, and then create masses of new journal files with different lecture/assignment/writing topics all piled together, but easily searchable. As a bonus, it syncs very well over mobileme, AND there's a windows version (which maybe even syncs over mobileme too?), so you can keep it handy. They have an iphone version coming out any day now.
In the CLASSROOM:
Timeline 3-D from BeeDocs: this does one thing very very well--create timelines in a very cool visual format. You can put them into Keynote very easily. It's on sale at this very moment as part of the bundle:
http://www.mupromo.com/
Tooble: this is a little program that downloads YouTube videos off the internet and leaves them as a file in iTunes. It makes using youtube material much easier.
Handbrake: this is software to rip dvds to disk. It's dicey in terms of intellectual property, but it means if you're using anything on dvd you can leave the dvd at home and have a permanent electronic version of the clip to put into presentations. Also, you can even edit the file Handbrake produces in iMovie, so you can clip out bits you want to present.
Bento: I've been all over the place on trying different software to keep track of students. Bento has a good interface and is good for entering records. Also, there's a good iphone application which can be useful. It lacks the calculation power of excel, however, so if you like using spreadsheets to keep track of grades eventually you'll need to export the records. Still, that's not so hard and I find it much more difficult to keep records clean than to tally things up at the end, and Bento makes keeping the records clean a lot easier. I'm very very curious about the ipad version of numbers. It looks like it has a good forms view which would make this use of Bento superfluous.
By the way, are you thinking about an iPad? I'm curious about that.
"Research applications" is entirely dependent on your field.
Not really. Writing in the academy is quite different from writing a novel, or a letter to your grandmother. Regardless of your field, you need to juggle a lot of different files and keep track of a lot of different snips of text. I think that's what the OP is getting at.
I've never tried it, but a lot of academics swear by DevonThink. Sometimes I fantasize about buying a SnapScan scanner from Fujitsu and scanning my file cabinet of copied articles. I have this image of being able to call up any article or copied source at any moment on my shiny new ipad.
Then I wake up.
Forgive the tsunami of posts, but I have an article to finish, and this thread is so much more fun than writing it.
Here's an odd one that I actually use a lot: ComicLife. It came free on my MacBook Pro. It is a desktop publishing program specifically designed to create comic book layouts. I use it and Omnigraffle with Keynote all the time to make shapes more interesting, but even more importantly, I am completely sold on ComicLife as a way of presenting ideas in a more friendly accessible fashion. A thorny philosophical quotation is so much more readable when it's in a speech bubble over a comicbook style picture of Kant.
