I tried using WP-ShortStat in the past, but stopped because I was getting tons and tons of referrer/referral spam, and all this spam was filling up my database.  I looked into it and found a way to reject referrer spam by using .htaccess.  I tried a few things out and it seems to be working great.  I'll be continually updating the keywords it uses to reject spam, but that's something that I'll probably be doing less and less over time.