If you have some lower quality sites do you leave analytics off them and just not claim them in Google webmaster tools?
what do you mean by lower quality? like autoblogs? i use GA, on sites that are typically whitehat in nature.
I meant a site that contains anything at all that you think they won't like:thin content, certain redirects,subject matter that they have been known to penalize, lots of affiliate links- any site that would probably not get a good quality score or rank high in the SERPS.
a So it sounds like if they are indexed, they're probably already penalized as it is - having GWT and GA on them wouldn't affect that process for better, or worse. Are they currently indexed on Google right now?
This was more a general subject than based on specifics. I do have some sites indexed highly although they are 'hope for one huge payday' rather than steady income as far as monetization. The issue is if you claim all your sites including ones Google doesn't like are they apt to penalize all your sites in the SERPs or ban your Adsense account because of the low quality sites, or conversely lower your quality scores if you are doing PPC with them.
To be fair, I think your question has evolved a little from your original. To your new and more targeted inquiry, I don't have a solid answer - if it were a specific issue, I would test it by creating another account for adsense and test having both one good and and a "bad" site under the same account to see the effects. Never done this myself, so I wouldn't recommend it with confidence. Hopefully someone here will be able to settle this one.