I did an interview together with Vanessa Fox, just before she left Google. We talked about what was going on with Google Webmaster Tools, features that people have been requesting, duplicate content, and the renaming of the re-inclusion request form to the reconsideration request form.
I was intrigued in particular by the renaming of the re-inclusion request form. Vanessa clearly defined this form as something to be used in the event that you had been violating a webmaster guideline, and that you had fixed it. Here is her exact wording:
That form is really for situations where you have violated the guidelines in some way, and you've fixed it. Then you can use those forms to have someone take a look at it as opposed to just waiting over time for things to naturally pickup again.
It's a fascinating statement. It suggests that you can send in an appeal for any penalty that you have become subject too (once you have fixed it that is), and the value of this appeal is not necessarily limited to appealing manually applied penalties. Keeping in mind Google's recent statements that ALL forms submitted with the reconsideration request form within Webmaster Tools (i.e. you are providing your identity as you make the submission) will get looked at, this is a powerful statement. Just be careful to really address the issues before you make the submission