Here's what I've got:
Chax is an add-on for iChat that seamlessly adds a ton of little touches to make the whole program a lot better. It blends in so well you forget it's there until you try and use iChat without it and miss all of its features.
NetNewsWire is a great free RSS reader that just recently started syncing with Google Reader, although it's in kind of a transitional phase right now, so it's slightly buggy, but I still use it daily.
Growl is a fantastic system for apps to give you notifications for whatever. It works with tons of 3rd party apps, and there are plugins to make it work with built in apps too. Chax, mentioned above, is one of them.
iConcertCal is another. It's an iTunes plugin-in (disguised as a visualizer) that searches your local area for concerts based on the music in your iTunes library. It can even give you Growl notifications if you play a song by an artist with an upcoming concert near you.
GrowlMail is one of the plug-ins that comes with the download of Growl and makes Mail.app give Growl notifications.
Alarm Clock is a very reliable alarm clock that can wake you up to your iTunes music, and has features like easy wake (slowly building the volume) and regularly scheduled alarms. One of the coolest parts is being able to snooze with your Apple Remote.
Flip4Mac is a commercial product, but there is a free basic version offered that allows you to play Windows Media files in QuickTime. This is really an essential, because Windows Media Player for Mac was abandoned years ago, and you WILL run into Windows Media files. I guess if you're a VLC fan it probably doesn't need this, but I'd highly recommend it.
And while we're talking about that,
Perian is a plug-in that allows QuickTime to be able to play a ton of formats that it can't natively. I never use VLC because with Flip4Mac and Perian, QuickTime's got me covered.
Handbrake's already been mentioned, so I won't go too into it, but it's great for ripping DVDs, provided you at least have VLC on your system (which is why I do).
Hulu Desktop is an official player from Hulu that allows you full access to Hulu and can be completely controlled with an Apple Remote. It's awesome.
Quicksilver is really powerful. I'm not even sure what I'd call it. On a basic level, it's an app launcher, but it can do sooo much more. A bit of a steep learning curve, but it can really pay off. It's been kind of abandoned by the dev, but
here is the last version. As time and the OS go on, more and more aspects get broken, but it's still extremely useful. There is some continued work since it was open sourced, mostly on cleaning up the code, but newer versions are available
here. Oh, and it's also one of the many utilities that provides Growl notifications for iTunes. If you decide to learn it, Google some tutorials. Lifehacker has some great ones.
Schoolhouse is really useful if you're a student. Supposedly there's a version 3 coming out, but the dev hasn't mentioned it in his blog since 2007, but I think it'll still come out someday. Even if not, I use version 2 for all my school organization.
Transmission is an awesome torrent client. The first choice of many a Mac user. Lightweight and simple, yet powerful.
And finally,
VLC is a media player that can play basically any format. Personally, I'm not a fan. I never run into files I can't play in QuickTime with Flip4Mac and Perian installed, and I think the interface is pretty terrible. Definitely very un-Mac-like. But tons of people swear by it. I just keep it around so Handbrake can do its thing on DVDs.
