Using software to manage your family history data is one way to make genealogy more like a hobby than a full time filing job. I have experience with two of the top genealogy programs for Windows, so what I write here is based on that experience and if you use something else, keep doing what’s working for you.
Family Tree Maker is the software that links closely with Ancestry.com, probably the biggest commercial online genealogy resource. And it is commercial! You will pay for everything you get but for some of us, it’s worth it. Family Tree Maker does a good job of navigating the resources on Ancestry.com and linking things to your family members. As a matter of fact, it’s so easy to link data to your family members that you need to be extremely careful that you review every resource before you merge it to your family tree or you can get a lot of so called “facts” that conflict and clearly don’t help you find the truth of your lineage.
The Master Genealogist is a software package that doesn’t try to link you to resources on the Internet. You have to find your own data and link it up manually. That may sound like a negative, but The Master Genealogist does a better job than almost any other package of documenting the research behind your family tree. It also has more ways to customize the reports you generate so you can, with effort, produce a product that is worthy of publication.
My conclusion — I use both of these and like them for their individual strengths. I do most of my online research in Family Tree Maker and then review everything before entering the data into The Master Genealogist. Entering the data twice may sound like extra work, but it gives me a way to check my work more thoroughly and I like that.
UPDATE RE: The Master Genealogist (Aug 1, 2014)
Right after I finished writing the post about software for family history research, I received a notice from the developer of The Master Genealogist announcing that he was ceasing development of the product in a few months. This is really a shame because there isn’t another product around that does what TMG does. Those of us who already have the program will continue using it as long as it works with whatever Microsoft turns out, but based on the recent news, I can’t recommend that anyone dive in and buy The Master Genealogist unless a new developer comes forward and takes over the product.