Here is a bit of a crazy question, but here it goes. I was doing some directory submissions last night for my personal blog. I used my personal gmail account or googlemail. Some of the confirmations ended up in my spam filter. If google mail is finding websites spam, does that mean that the search engine shares that data and it isn't really a site you want to be submitting to?

Not necessarily - the spam filter on gmail/googlemail or any other spam filter usually includes standardized messages such as the ones a directory generates. It's not necessarily seeing the domain/website as spam, but rather the contents of the mail involved.

I could see this being an issue if a site produces a vast amount of 'questionable' mail, but under reasonable circumstances I doubt it would be a problem at all.