My personal suggestion is what I currently use on my servers. Its a program called 'webstats'. Technically its actually a perl script that runs analog, and report magic, to generate stats for every vhost on a server, as long as its in a certain directory, specified. It's actually pretty powerful. If you want an example, check:
From what I've seen it isnt too bad. The primary server it runs on is fairly fast (2ghz AMD, 1gb ram). When the stats runs, cpu usage jumps to about 15-20% from its usual 1-2% for about 5 minutes till its done. I agree it could probaly be faster, but it works, so I cant complain.
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