Hi everyone, glad to see this thread is remaining popular. Just to address the quote above in case it concerns anyone, the portal page and tor site are completely separate and neither can be traced back to any physical persons at Silk Road in any conceivable way. The portal page was an afterthought to get more traffic to the site, but did its job too well, over-exposing Silk Road. We will reopen it when we feel like the site is ready for that kind of exposure.
If you say so.

On another note, I would like to bring this thread back to the "Feedback requested" part of the title. I am especially interested in hearing from anyone with alot of experience in network security about how to improve the anonymity of the site beyond running it as a tor hidden service. How would YOU do it? What are some worse case scenarios?
There exist attacks which can potentially locate a hidden service. Therefore, make sure the server it's running on is also paid for anonymously, and can be relocated quickly if necessary.