I use several tools for rank tracking:
1. CuteRank - Simple and easy to use keyword rank checker and best of all, it's free. http://cuterank.net/
2. Market Samurai - Great software for keyword research and includes a keyword rank checker. http://www.marketsamurai.com/
3. SEMRush.com - I don't really use this site for keeping track of my keyword rankings over time, but it is invaluable for discovering new keyword opportunities since you can see all the keywords your site and your competitors' sites rank for. One way it helped me is that on one of my sites, I discovered that a random PDF was ranking #1 for a popular keyword but since I was only using Google Analytics to track my website visitors, I had no idea the PDF was getting any traffic. So I redirected the PDF to an actual page with the GA tracking code, website navigation and a contact form in order to convert some of those visitors in potential customers.