GameTracker at www.thegolfchannel.com I think you can use it for free but not get to use some of the stuff that is available for $30/year. I quit using it probably about a year ago.
A lot of the online handicap trackers also allow you to putt stats such as fairways hit, driving distance, sand saves, greens in regulations, etc. etc. etc.
www.freegolfinfo.com has a Game Tracker forum for free that I use to record my rounds. They have an enhance version that your pay an annual fee for but the free one is more than adequate for my needs.