Taking notes is very important as it forces you to think twice about the information as you write it down using your own words ("copy-paste-and-dump" information does not have the same learning effect).
In addition, you use different "senses" (writing in addition to reading) which enhances learning.
And of course (unless you only write it down on paper) you will be able to search for it and find it again when you need it (because you will not be able to remember every detail).
So, it isn't that important which tool you use, as long as you keep most notes in one place (so you know where to look for it later).
(shameless plug)
Of course, as the number of notes grow, many people will experience information overload and have trouble finding the forest for all the trees...this is where using specialized tools that are optimized for finding what you need will help you.
In addition, you use different "senses" (writing in addition to reading) which enhances learning.
And of course (unless you only write it down on paper) you will be able to search for it and find it again when you need it (because you will not be able to remember every detail).
So, it isn't that important which tool you use, as long as you keep most notes in one place (so you know where to look for it later).
(shameless plug) Of course, as the number of notes grow, many people will experience information overload and have trouble finding the forest for all the trees...this is where using specialized tools that are optimized for finding what you need will help you.
My blog post regarding large amounts of information - http://www.ppcsoft.com/blog/iknow-efficiency-scalability.asp
(/shameless plug)