The recent site problems were due to thousands of spam comments every day, coming in too fast for the system and the database to cope with. I guess that’s the price to pay when a site starts to become popular. What I did after repairing the database was:
I deleted more than 8,000 spam users, disabled new user registration (please write if you want to register a user here) and added CAPTCHA protection to the comment form.
I think this will eliminate almost all incoming spam. Unfortunately the CAPTCHAs may be annoying if you want to post comments. These are reasonably simple to read and type (I hope), please write if you have any problem. We need CAPTCHAs, but I want to choose a very user-friendly implementation.