Secrets is a (free!) preference panel which has collected a bunch of these settings and made changing them as simple as checking a box or choosing from a drop-down panel of possible choices. It includes settings for about 40 different applications, from Apple applications such as Mail, iCal, iChat, Finder, Front Row, Keynote, DVD Player (and more) to third-party applications including Adium, Audio Hijack Pro, BBedit, EyeTV, VMware Fusion, and TextMate (just to name a few). Some applications have a lot of hidden settings, and some have only one or two.
If you see a setting but don't know what it does, click it and Secrets will show a brief explanation (these are also available on the Secrets website, but they are easier to read in the preference panel). If you change a setting which requires you to restart the application, Secrets will tell you, and even give you a "Quit This" button. (It's usually best to make these changes when the app isn't running.)
Unfortunately at least one of the secret settings from 10.5 doesn't seem to work in 10.6. That is, the setting to turn HelpViewer into a regular (instead of floating) window. There may be others.
I'm off to explore and see what new goodies Alcor (the developer of Secrets, who you may also know as the creator of Quicksilver) has uncovered.
Thanks to the recently-revived Hawk Wings site for bringing this to my attention. If you use Apple's Mail.app, Hawk Wings is a great site for tips and information.
Update: We seem to have taken down the Secrets website (oops!) but you can download the preference panel from a mirror (zip) (166kb).