Genealogy software is the best way to organize your research. Here are some options:
  

Family Tree Maker. This is what my wife and I use. Honestly, we did not evaluate all the options. Nevertheless, we have found Family Tree Maker easy to use. The 2008 version has several useful upgrades. Click here for more information on Family Tree Maker at Ancestry.com.

Family Tree Legends. This is downloadable genealogy software that has several useful features: Real-Time Internet Backup to preserve your data, Real-Time Internet Publishing that keeps your data on GenCircles up-to-date without having to upload GEDCOM files, Smart-Matching of your entries to the GenCircles global tree, and Webfacts to give your related facts in your file such as information on place, date, event, or name. The software also provides the common genealogy charts, indexing, reports, etc. Click here for more information on Family Tree Legends.

Personal Ancestral File. This is available as a free download. It does not have the full range of capabilities of Family Tree Maker. Click here for more information on the Personal Ancestral File.

Also see

Genealogy on the Internet