Just wondering if anyone thinks/knows if having hundreds of sites on one Webmaster tools account in Google sets you up easier for penalties? For example, for similar made for adsense sites within the same niche?

probably not the smartest thing to do.

I wish I would have never signed up for webmaster tools

I was wondering the same thing, should I register my newer domains in new accounts? I'm not sure what difference it would make. I did recently delete all of my analytics stuff from all of my sites, so I'll see if that makes a difference.

I would try them on differant accounts just to be safe.

I think using web master tools is just making it easier for Google police to watch you and penalise you. I also think if you have one site that has penalties they will be less forgiving on your other sites.