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Hello, I'm one of those people that got the "unnatural links" message from google. Since i run my site from the very first day and always was a one man business i know all the ins and outs of the website.
Basicly i have  never ever used a seo company to submit my site anywhere.
Never ever i used any shady tactic to get better ranks.
The only thing i did was trading traffic/links with real active websites, being daily updated, high traffic, etc etc. So. After i got notified in webmaster tools i started digging into a list (provided by webmaster tools) to find out why i got this message (meanwhile i lost 75% of my se traffic in past 3 months) After searching for hours i found out that in the past 2 / 3 months my site has been spammed on about 150 forums (completely dead forums with nothing but spam on it) There was no logic at all since my site got linked with the most ridiculous and unlogical word phrases.  
My site is adult related and all spam links contained word phrases like "bangladesh mobile"  or "rock girl"  or  "animal abuse" or "ringtones" etc etc. if i ever would be so stupid to start spamming my 7 year old strong business i would at least use titles that would make sence. anyway.
I can't do nothing about these forums, i don't own them, i can't erase them and if there are any owners, they simply don't respond.
I made a list of all the forums and send it to google but the only response they come up with is "there are still unnatural links". I hardly believe they did anything with that list i send them. I don't know what else i can do and was hoping that somebody could advice me on what to do here besides sending google messages on a daily base. cheers