Saving handwritten notes for future reference I have more than one hundred pages of handwritten notes. 

I made these notes while writing different chapters of my PhD dissertation. The notes include summaries of journal articles, my thoughts, suggestions by others and anything that I thought could be potentially useful for my research.

I am wondering what is the best way to organise and store them. Converting them into pdf is one way of doing it but I want to organised them in some way e.g. by chapter, or date or key words.

Is there any program or software that can be useful in this regard?
It's not an answer, but it's too long for a comment…

I have one word for you in the future: Moleskine. Good quality notebooks, organized either thematically or chronologically, is a great way to store that sort of information. For notes, long term conservation is a big issue, and you have little guarantee that bells-and-whistles software X will still be working on your computer in 10 to 20 years. Simple solutions (both electronic and not) are the best for that purpose. 

Finally, I have managed my notes electronically for some time (I tried many combinations, including iPad/Evernote/Dropbox, text files, LaTeX), but wasn't satisfied for the reasons above. I went back to dead wood storage (aka paper) with delight!