If you have a Restore Point, you could revert back to a time before the reg cleaner was installed and or used. Or if you have backed up Vista at one time or another, then use the backup.
You have made the wrong assumption that many others have and that is to apply a cleaner to the registry. Vista and Win7 have a different registry matrix than XP and requires no such utility. Most geek sites will plainly state that these utilities do more harm than they actually say they fix. Stay clear of them, especially if running Vista or Win7. If you must use a light cleaner such as Ccleaner
http://filehippo.com/download_ccleaner/
#NOTE: During installation of Ccleaner, un-check any toolbar offers or the like as these sometimes cause undesired effects to your browser.
If you cannot restore your registry to a working condition you may want to do a factory restore or, if you own a full Vista Installation Disk, then a clean install is the way to go.
Cheers...gwb56
#EDIT: If you're receiving pop-ups, it's a good chance that spyware was included in the registry cleaner tool. Download, install, UPDATE and run a quick scan with MalwareBytes AntiMalware (MBAM).
http://filehippo.com/download_malwarebytes_anti_malware/