If you are seeing 1/3 of the flops, you might want to try tightening up a bit. I'm seeing 16% at 100NL on FullTilt.

Also, how's your aggression? Are you limping in a lot, or do you usually raise pre-flop? You in multi-way pots, or usually just 1-2 opponents?

As far as software, I highly recommend Poker Tracker. Well worth the 56 bucks or whatever to buy it. They'll let you download the software and import 1000 hands for free to check it out.