Genealogy Software
I'm not sure what is more important for organising your research, your paper file system, or genealogy software. I think the easy answer is to do both and keep them both up to date.
The next question is what software? There are quite a few choices which are all good. Below I recommend 6 different systems which I feel are all in the excellent category and can't go wrong with. I have not used all of these. The last 2 I spent a lot of time reading their documentation and looking at screen shots on their web sites. I am most familiar with Legacy and PAF.
All I've done is narrow the choice down to 6 options which you can't go wrong with. What now? Many of them offer limited functionality, or limited time period versions for free, or in the case of PAF is free. Nothing to loose there. Try one and if you don't like it, try another. Or try one and then another, and decide which is better.
I use Legacy for my family research, and export to PAF regularly to use some features of PAF Companion. I also do this to confirm my data from Legacy remains portable. Why did I choose Legacy? The view I use the most is the family view. I like the look of the family view using Legacy in terms of amount of information displayed, how it is arranged, and how I can alter the look. They have good features and are continually improving their product (as all the others are too!). Source management is also extremely important, and Legacy does this very well. They have some very nice features for entering large amounts of source data. Though this is an advanced feature and took me a while to learn.
I recommend you visit the web sites of the 6 software packages below and choose the one that you think looks the best. You can't go wrong. If you still can't decide, then I recommend what I use, Legacy.
RootsMagic
All the standard features. Look and feel okay. Family view a bit cluttered, but fine. Nice reports and extra features, especially the publishing features such as the CD creator, and wall charts.
Ancestral Quest
All the standard features. Look and feel okay. Don't like the family view. Web page creation about same as others, but with nice scrap book feature. Excellent features for working with sources!
Legacy
All the standard features. Look and feel good. Nice advanced features. My preferred family view. Nice reports, but a bit weak on the fancy presentation type charts. Excellent tools for working with sources.
Personal Ancestral File (PAF)
PAF along with PAF Companion are a good tool set. I'm not as fond of the look and feel. I found it difficult (if not impossible) to customize the information I'd like displayed. But it has all the basic features needed, and is free! You need PAF Companion to get any more advanced non essential features.
The Master Genealogist
Strong software with all the expected basic functionality and advanced features, including web page creation and nice looking reports. Without installing a trial version I could not fully access the family view look and source management. From the documentation it looks very strong. The documentation seemed a bit denser than the others. From the very small screen shots I don;t think I like the look of the family view as much as Legacy or Family Tree Maker.
Family Tree Maker
All the standard features. Look and feel good. Family view similar to Legacy, and is very good. Their web page does not make it easy to know what their advanced feature list is, and I can not comment on source management - one of the most important features.