Just so the Googlers know...
This thread is old, but I thought I'd drop my two sense in because it was the first link on my Google search.
The certificates are all located inside of Tools > Options then the Advanced tab (all the way to the left) The the Encryption tab. You'll see a button labeled View Certificates
The certificate one is probably trying to delete will be located in "Your Certificates" or "People." There's a chance it'll be listed inside of "Servers" but you more than likely don't want to delete anything in the "Authorities" list, because these are the root servers the system is using to verify other servers. I suppose you could catch some terrible bug that would frig those up. In that case, though, I'd probably try deleting the above files.