Well... Basically there's the easy and the difficult part.
And for users who, like in OS 9 and earlier, put things all over the harddrive, the following list does not apply. If you're such a person, just make sure you REMEMBER where you've put your stuff. Chaotic people, those.
For backing up, I advise to backup everything. CCC to an image, for example. But other backup solutions can achieve the same. Takes a while, but you've _got_ everything backed up afterwards.
Then you install the system. Easy, too.
You then best setup the users with the _same_ shortnames as before (unless you've gotta add some) and give them the same rights etc. as before the reinstallation.
Then you replace the contents of the new home folders with the stuff in the backup. Everything. You can do this in the Finder (by loggin' in as the user in question to keep the user rights intact) directly. Just make sure you logout right after the copying is complete, so no application tries to overwrite the prefs files you just copied over.
After all the users are in place, there's basically the following:
1.) /Applications/
You just choose any third-party application in the backup's /Applications folder and hit Cmd-C. Go to the new installation's apps folder and hit Cmd-V. Same for apps in the /Applications/Utilities folder.
2.) /Library/Application Support/
You'll find a lot of stuff here. Basically, copy everything over that seems to belong to applications you still intend to use. The folders are named after the developing companies, AFAIK. Depending on the installed apps, you might also want to check whether there's /System/Library/Application Support/. On my systems, there isn't such a folder. So nothing to copy.
3.) Check the applications and settings. If the applications don't want to run, you have to reinstall them. Don't have to delete them, usually, just install them over the already installed versions. There simply _are_ some apps that don't "behave" well here. Xpress, as far as I know, needs to be reinstalled, for example.
4.) Fink and other UNIX stuff
I don't know about fink. Maybe there's a way to just copy things over (_should_ be in my opinion), but probably you'll need a newer version of fink for a newer OS X version and you maybe even want to recompile the stuff with the newer GCC version?
Your hand-tooled configuration files for Apache and other things, you'll want to just copy over from the backup.
I guess my way of backing up and reinstalling isn't ever going to be simple, since it basically mixes a fresh install with several 'parts' from your old system (although nothing that could hurt the new system) - and those depend on the user, really.