How to read and take notes on research papers
This probably isn't an ideal solution; but I still find it to be the most effective in the long run:

I simply keep a log of what I read, and I specifically do this using tex. That way, you will have a searchable document for any words that you may be looking for in your notes. You can also use the makeidx package to add an index to your text document, which lets you "tag" sections of your documents with various keywords. I also make sure to cite what I read, even if it is for my own purposes. This is especially useful when you are writing a paper, since most of your references will be ready in bibtex format.

It took me a while to get used to, but I find it very nice to have a well organized research log.

Since requested in the comments, given below is what the log looks like. I don't want it to become a full latex document, but it should be sufficient enough to give you an idea. Note the index markers, which are basically "tags" that don't show up in the text.

\section{Paper #1 Name, Authors, Date, \cite{...}}
My summary of the motivation and findings of the paper, or whatever I find interesting/useful.
May be as short as a few sentences or as long as a page, depending on how relevant it is. 
\index{an important word}

\section{Paper #2 Name, Authors, Date, \cite{...}}
Same thing here.. \index{another important word or two}

\section{Paper #3 Name, Authors, Date, \cite{...}}
and so on..

\printindex


Then you can look up your page numbers in the index, which is included at the end of the document. For more information about the package, see CTAN and Wiki.