If a site is being penalized for duplicate content, and you remove that content, than will Google remove the penalty next time the bot comes around or do you have to contact them personally? The reason I ask is because I think I am getting this penalty for my affiliate part of the site that is just a dynamically generated template and if you do a search a lot of other websites use it as well.
IF that is what is going on. You will most likely have to wait a few months before they remove a penalty. I had a site that seemed as if it was getting penalized for duplicate content and it took a few months before Google put it back in the search results. What exactly do you see them doing? Are they not sending you search traffic or are they not showing certain pages of your site with a site: command or something?
I just rank no where for my main keyphrase and rank somewhere in the 200s for really un competative keyterms Also, if I do decide to get rid of all the dupe pages. What is the best way of going about removing the 1000s of pages from Google's index? Should I just delete them from my server and let them die naturaly, or is there a faster/better way?
Doesn't sound like you are getting hit with any duplicate contnent filter. If you used to rank better for a competitive/non-competitive term, and the site is new, you were most likely enjoying what many "new" sites enjoy in Google. Now that the honeymoon period is over, you are back where you "should" be. If the pages in question were not cached, then I might think there was some kind of dupe filter working on your site. But, "poor" rankings are definitely not an indication of this AFAIK.
Well, I don't know your whole situation, but I have been "hit" with a number of things over the years. It doesn't sound to me like you are being penalized for anything. Sounds like you need to get on some SEO and be sure not to go overboard. When in doubt, use moderation.
Are you guys speaking of duplicate content on different pages within 1 website or other websites with duplicate content linking to your main site?
<<affiliate part of the site that is just a dynamically generated template>> can you just stick that in an iframe, and surround it with your own original content? GEM