[I have a site that I created about a month ago and for the first two weeks it had been sitting about spot 15 I kept building links to it and now it is in position 600 and something I was just wondering if it is possible that I am being punished for having a Nofollow link to an authority site (Wikipedia) I also have the link the same color as the text on the page and I don’t have it underlined. Essentially the only way to know it is a link is if you were to mouse directly over it. Can this cause me to be penalized?]
No! Linking to Wikipedia will not cause your website to be penalized.
There is no reason you should consider your website to penalized, it’s not de-indexed, it’s not penalized.
Google cares about its users. Google will hold you accountable to what type of content you place on your website, including where you link out to. A page loaded down with spam that links out to malicious, virus-infected websites will certainly suffer from the lack of moderation, up to and including being de-indexed. Using the Nofollow attribute on your OBLs doesn’t completely immunize your website from scrutiny.
Natural links are not called “natural” based on the Nofollow attribute, and most natural links are not links with the Nofollow attribute.
Here is a more conventional explanation of “natural” links.