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In the meantime, add lots of good content to your site.
Otherwise, you'll have to just move on to a new domain.
How do you know that you've been penalized? Do you know that you were doing something against Google's TOS? Sometimes it is tricky and you think you've been penalized when it might be a simple back-link or server-side problem. How many back-links did you have to your site in September?
(If you are convinced, you are PR0 because of a penality, not to make you feel bad but recovering from PR0 is sometimes impossible. Depends on what you did wrong.)
a new type of link directory which was more automated
Google has big problems with automated link directories, especially if the "add your link" function is automated. Depending on your implementation this is the first thing you might want to take a look at.
I do realize you said your other site with the same directory software was not affected, Google doesn't always catch everything and everyone at the same time.
Not true, every chance....but it takes a while.
Put the PR0 site on the back burner, it probably does good in Inktomi and ATW anyway?
Get a new domain for Google, change the site content a tad, get the backlinks again and let the puppy fly.
10 to 15 months from now the old PR0'ed site will reappear and then you will have two good Google performers and probably two good Inktomi performers.
At which time everyone will call you a spammer....live with that;)
On my site it says "add a listing." I have another site which I started around the same time the other went down. It uses the same type of link directory with automated "add a listing." So I am not sure this is the problem.
Emphasis added for emphasis
I'll simply repeat it, this time with emphasis:
"Google has big problems with automated link directories, especially if the "add your link" function is automated. Depending on your implementation this is the first thing you might want to take a look at.
"I do realize you said your other site with the same directory software was not affected, Google doesn't always catch everything and everyone at the same time."
Whether this is what is causing the penalty now is almost besides the point. This is something known that Google looks at very, very closely. It's only a matter of time until G hits the second site. Please, take care of this now before you dig yourself a bigger hole. If you do clean it up now and it was the cause of the penalty the one site should return to G's good graces in a matter of time and the second one might not get penalized.
Does removing the "new!" text that is 1 year old help? In any case, I didn't add very much text but cleaned up the interface and tried to make it more visitor friendly, and removed all the useless meta tags.