Baltwo is, as usual, correct.
If you do an Erase & Install, then transfer from your TM backups, you have some options about what to restore, in general categories, but you can't pick and chose individual items. To leave some apps behind, you'd have to chose not to transfer any apps, then after you restart, use the normal Time Machine interface to restore the ones you want.
Assuming that you transfer users, that would also bring over all the items from the home folder(s), such as preferences and data files, related to the apps you did not move. While these won't cause any performance problems, they may take up more space than the apps.
Your best bet may be to start "thinning" out the stuff you don't want. I'd make a ToBeDeleted folder, with Applications, Preferences, and Application Support sub-folders (and others if needed). For a few apps you don't want, move them and their related files into the corresponding sub-folders, so if things go wrong, you know what to move back and where to put it. If nothing goes wrong for a while, then copy that folder to CD/DVD and delete it. Then do it again for another group of apps.
Being paranoid about this sort of thing, I'd be inclined to make a couple of copies of each CD/DVD, take one to my safe deposit box, and keep them for a long time.
