I had a similar experience when my 80 page site disappeared. I am not sure exactly what caused it but I was a member of a small webring of engineering sites and one of them was considered to be a bad neighbourhood so it was probably this.
Anyway my site was dumped on 30 January 2004. When I realised what was happening I contacted them on 2 February. I got a standard reply saying that my request had been passed to their engineers. (From then until the end of March I wrote/responded to their replies a total of twelve times.)
On 17 March my PR5 was reduced to 0 and I contacted them about this. Once again I got a standard reply requesting that I be patient and stressing that they had passed my request to their engineers. They also said that if their engineers took any action it could take six to eight weeks for this to be reflected in the search results.
At the beginning of April my site came back with it's proper PR but it was nowhere to be found in the rankings. There were signs that it was creeping back up but I was still getting no traffic. Suddenly, on Saturday 8 May it leapt back to near the top and through last week it improved further and I now have the number position for my main KW.
All I can say is that during this waiting period I did everything possible to ensure that my site was squeaky clean. I also added and updated content, etc. and now that it has returned I hold better positions than before.
Conclusions? I believe that I did incur a penalty of some sort. I also believe that Google listened to my requests for reinclusion and that their engineers did something to get me back in.
Advice? Hang in there, ensure that your site is clean and get in touch with them again if there is no sign of it reappearing.