ProTools is the industry standard digital recording software. With ProTools, you can do just about anything with your recordings. However, ProTools is very expensive and extremely complicated.
Cubase does not have all of the options that ProTools offers, but many guitarists consider Cubase one of the fastest guitar recording tools. Again, Cubase is an expensive program, but it is a popular alternative to ProTools.
If you own an Apple computer, GarageBand is perhaps the best way to record your guitar. Not only is it free (with purchase of the computer of course), it is also relatively simple to use and can yield professional results.
Audition is a PC program that gives similar results to GarageBand. While Audition does not come free with PCs as GarageBand does with Apples, it is still cheaper than ProTools or Cubase.
Audacity is a free, downloadable program that works across all platforms. It does not have some of the features of higher-end guitar-recording software, but it does work very well.
Other popular recording programs include Sony's Acid Pro, Ableton Live, Logic and Cakewalk Sonar. Each of these programs has its own strengths and weaknesses, so before throwing down hundreds of dollars on a program, do your homework.