A while back, I worked with a smallish hosting company to help them implement a solution to this. The system I developed examined web server logs for excessive activity from any given IP address and issued firewall rules to block offenders. It included whitelists of IP addresses/ranges based on http://www.iplists.com/, which were then updated automatically as needed by checking claimed user-agent strings and, if the client claimed to be a legitimate spider but not on the whitelist, it performed DNS/reverse-DNS lookups to verify that the source IP address corresponds to the claimed owner of the bot. As a failsafe, these actions were reported to the admin by email, along with links to black/whitelist the address in case of an incorrect assessment.
I haven’t talked to that client in 6 months or so, but, last I heard, the system was performing quite effectively.
Side point: If you’re thinking about doing a similar detection system based on hit-rate-limiting, be sure to use at least one-minute (and preferably at least five-minute) totals. I see a lot of people talking about these kinds of schemes who want to block anyone who tops 5-10 hits in a second, which may generate false positives on image-heavy pages (unless images are excluded from the tally) and will generate false positives when someone like me finds an interesting site that he wants to read all of, so he opens up all the links in tabs to load in the background while he reads the first one.