The Other Game Company (TOGC) offer Blank Cards to note or print all relevant and reoccuring NPCs, Items, Towns, and other Areas for easy and quick access during the gaming session. The times of shuffling through all your handwritten pages and txt files on your laptop in search for the eye-color of your never-dies-and-still-annoys supervillain on the climax of your adventure are over.

All Cards are 2-sided with combat relevant information on the front side and background notes and skills on the back, for the Character Cards. The Gamemaster Cards for NPcs feature general appearance and goals/motivation on the front and a little stats box along with a notes area on the back.

For ease of use the pdfs are editable, so you can fill them out and then print for a clean overview of all your premade NPCs and leave some blank for on-the-fly note taking.

http://www.theothergamecompany.com/freestuff/blankcards.html

in the free stuff section you can also find a printerfriendly version of the official dnd 3.5 SRDs

I’ve been using the portable and super easy to use TiddlyWiki for general note-taking throughout our campaign. TiddlyWiki needs no installing, but a javascript capable browser the markup is very intuitive and all the information is saved into one single file.