Most of the posts here at Free Genealogy Resources show you where to find data on your ancestors. However, we haven't talked much about how to go about finding the information you seek or how to deal with it. The other day, I came across a blog post at Susan's Genealogy Blog that gives a great step by step guide to research from starting with your objective all the way to filing your results.
While the guide is geared towards genealogists researching at libraries and archives, it still has some good information that even the at-home budget genealogist can do.
If you need help developing a research plan, check out Ancestry's Learning Center article, Plan Your Attack.
The Board for Certification of Genealogists (BCG) has an excellent article by Elizabeth Shown Mills in their skill building section under Analyzing and Reviewing Published Sources that will help you perform a thorough analysis of your findings.
If you haven't yet implemented a filing system for your genealogical data, there's plenty to choose from. DearMyrtle has an excellent series on organization. Legacy Family Tree Webinars has a webinar by Karen Clifford on Organizing for Success (about halfway down the page at the time of this post. Kimberly Powell, the About.com guide for Genealogy has written a good article on Organizing Digital Genealogy Files.