ROM Cleaner's back-up tool will back-up: mail settings (including inbox), bluetooth pairings and wifi access point keys; apks found in "/data/app"
the apps are saved in "/sdcard/ROMCleaner/FirstBoot/data/app"
so you could take a look in that folder and decide to remove some apps
no settings are saved for the apps, and after a full wipe there shouldn't be any settings for those apps
to my knowledge most back-ed apps are not stored on the flash but on the sdcard, so no issues with ROMCleaner restoring apps that you only had backed up with some other app
so, the only problem would be frozen apps
in any ways, I like this tool, very handy, first boot will take a tad longer with all the apps installed, but no more setting up google, download Titanium (MBP in my case) to restore apps, since they're already there