They aren't exactly system tweaks like TinkerTool, but here are some goodies I use:
Butler. It lets you quickly access apps, files, URLs, whatever (I just use it for apps, personally) by typing a few letters. I also use it for quick access to a web search bar. I have it set to control-option-W brings up a little search window, which lets me choose any engine I want (I use it for MacUpdate and dictionary.com a lot), and then it'll open my default browser. Very handy. It has tons of other functions, too, but those are what I mainly use it for. It's free.
ChangeDesktop. It's a powerful desktop picture randomizer. I have thousands of desktop backgrounds, sorted in many different folders. The Desktop preference pane just can't handle it. ChangeDesktop lets me have it automatically pick a random background at specified intervals or on demand via its handy menu extra. Again, it's free.
Backlight. Another desktop background utility, only this one lets you do something completely different: run any standard OS X screensaver as a desktop background! Very, very cool. And it doesn't hog nearly as much CPU time as you might think, since most screensavers make full use of Quartz Extreme, offloading the heavy work to your graphics card which would otherwise just go idle. I often it with the "Pictures" screensaver (which I've customized to use my own library of backgrounds). Keep in mind, however, that it might send your fans into a frenzy after a while, and if you're on a laptop, it'll make your battery cry for its mommy. Once again, this is free.
Sizzling Keys 4 iTunes. A very simple and efficient way of controlling iTunes from any app with the keyboard. I have it set so control-option-left/right arrow will move to the previous and next tracks, and I have F5-F8 mapped to Play/Pause, Mute, Volume Up and Volume Down. It also (optionally) provides feedback on the current song. And yep, it's free, too.
GmailStatus. It's a menu extra that shows how many new messages you have in your Gmail account, and lets you quickly open your inbox in your favorite browser. Free.
And last but not least, PithHelmet. It's an add-on for Safari that adds powerful filtering capabilities, plus some other very cool features. I use it to block ads, transform URLs (for example, if I type "d word" into my address bar, I have PithHelmet set to transform that to http://dictionary.reference.com/search?q=word), and even alter the source of incoming pages before Safari renders them. And yes, it's free, too.