It depends on what you want. Also a slight warning, recently there was a topic here on Surfulator getting a price hike and UltraRecall no longer being developed so you might need to get your feet wet on those first if you're considering them.
Evernote and OneNote are the overrated ones you'll hear alot so they're good but not the best if you need simpler or more advanced needs. (I know that sounded oxymoronic but both of those apps toe the line but doesn't really cross either areas)
Another popular beta product here is InfoQube. High learning curve though.
Other popular ones are:Notetaking:
1. Google Notebook
2. Zoho Notebook
3. MindManager (Mindmap)
5. Online Wikis (most popular casual one I know is Wetpaint)To do list:
1. MyLife Organized
3. OmniOutliner (Mac)
4. Remember the Milk (and it's many plugins for FARR, Gmail, etc.)
P.S. Note these are just the popular ones. In no way are they the best for your needs. In fact, I only use two programs in that list I mentioned.
You may also prefer tweaks: (Use at your own risk!)
1. To do list on your desktop:http://lifehacker.co...r-desktop-213280.php