Besides Terminal.app and Mail.app, there are a few Mac OS X applications I can't live without. Not all of them are bleeding edge or extremely popular, but they all deserve some attention from Mac users who appreciate clean, simple and easy to use tools. So without further ado (and a tip of the hat to High Fidelity), here are my personal Top 5:
I've actually taken to using VoodooPad Lite to draft most of my weblog entries. As a simple text editor it can't be beat (although I sometimes wish it had a quick "remove formatting" option), and as a hyperlinked notepad it allows me to maintain quite complex sets of little notes and jump between them (a Wiki like mine is great, but an offline hyperlinked notepad can be a great timesaver).
And, as a nice bonus, it even lets me execute scripts straight from the "pad" - a little-known feature that I use to keep not-so-frequently-used command lines ready.
All in all, it's simple, totally uncluttered (you can remove every single toolbar and have just a plain window with your notes) and not in the least bit restrictive (I don't miss any of the features of the "full" version). A must-have.
The editor previously known as Hydra, and which is best known by its Rendezvous-based concurrent editing features - having everyone edit the meeting notes is extremely handy, I'm sure, but I will only believe it when I see a companion Windows or Linux version (there just aren't enough Macs around at my office).
I use it to do some coding, of course, but mostly for another little-known feature: its ability to quickly convert between several sorts of line encodings (CR+LF, LF, etc...) and between several sorts of character encodings (ISO-8859-1, UTF-8, Windows Western, etc.).
One of the not-so-many Mac OS X VNC viewers, VNCThing seems to have been abandoned - I cannot find any source archives of it, otherwise I'd probably host and maintain it, because it is the only Mac VNC client that seems to be able to deal properly with non-US keyboards when connecting to all my UNIX boxes - all others have either very flaky "dead key" support or feel like (very) poor implementations.
Mail.appetizer is the most useful add-on I've yet to find for Mail.app. It's not a standalone application, but it plays a big role in my daily usage, since it displays a transparent mail notification on top of your screen with a short message preview every time new mail arrives in your inbox - an Outlook feature I've found indispensable.
Despite its development being apparently halted, I've customized mine to be somewhat smaller and more discreet, and it has worked flawlessly with every version of Mail.app yet (including my custom hacks).
Last but not least, nothing even comes close to replicating the ease with which Quicksilver lets me find and manipulate applications and documents. I've previously written about it at length, so I won't explain everything here. Let's just say it's the icing on the cake, and that you should try it out for yourself - it almost makes the mouse redundant.