There are a lot of tools out there, mind maps, notes taking apps, list managers or some uncategorized solutions
I will start with the most common and popular tools and will add some rare apps to the mix in the end.
Is the first thing that usually comes to mind when talking about notes taking app. Great application, available on different devices, sync all your content from everywhere to everywhere. If you want to organize things, you need some discipline to keep things in the proper folders and use tags if you want to implement a more sophisticated system. Has support for audio records, some kind for drawing system on the phone. Browser plugin can be handy as well to save things you may find on the internet
Very unique list manager. Simple design and interface, but at the same time very powerful if used properly. Allows to hide complexity or regular notes by using a hierarchy.
Probably the best online mind mapping tool out there. One of those that have better design (but not an apple quality type) and it's built with relatively modern technologies (no flash).
Online solution to make all kinds of diagrams. Similar to MS Visio, but works in browser on any platform.
Read it later solution, it also works better than regular links managers.
Very good looking task manager. Was recently sold to Microsoft, so be expected to see it soon included with the next version of Windows.
The best Android mind mapping app that I could find so far.
Mind mapping (and or concept mapping) online app. Has a unique design, but was built with flash and can become slow if the map is getting too big.
Presentation software, very different from anything out there.
Very unique approach of storing and navigation information or to be more specific - thoughts. It's not a mind map, it's more like a group of ideas. It is mostly a desktop app (for different platforms), but the interface is not so easy and somewhat ugly.
One of the best text outliners.
Very sophisticated diagram builder, has a lot of functionality, maybe too much. Looks like a popular solution in the corporate world.
New and interesting solution, mostly focused on sticky notes placed on different canvases. Can be a great tool for brainstorming sessions and sticky notes lovers.
Mind mapping online app with some unique features, like an attempt to connect mind map and spreadsheets, where you can assign numbers to different nodes and run calculation number
Other mind mapping apps
mind42.com - simple and free, maybe too simple. mindomo.com - powerful, but very complicated. mindnode.com - only for Apple devices, loved by some
Promising but not really there yet
a way to visualize all the information stored in the cloud; good idea, ugly implementation
This list is not complete
Some of the apps I didn't include on purpose, especially those that are not much different from what was listed. Let me know about "good" tools that I missed.