Gameology: Commentary and Resources for the Game Studies Community

Admittedly, I haven't tried Endnote, but Zotero has been my citation manager/note taker of choice. It works right in Firefox, so it's really convenient. It does have it's limitations, but most of those can be worked around, and it's advantages outweigh those (mostly) minor inconveniences.

I think a Blog is also a great way to keep track of stuff. I haven't updated mine that well, but I do have a dissertation blog.

The other tool I use a lot for notes and general outlining is Netvibes. I use it like a wall of sticky notes where I can tack ideas and rearrange them periodically. It's also accessible anywhere, so that doesn't confine my work to a particular box, which I like.

Finally, another tool I experimented with, but never got the hang of, is FreeMind, a "mind-mapper". I showed it to my students, and at least one really got into it, so it's useful to some people.

Anyway, hope that helps. I really like learning about productivity/research, so let us know what else you end up using.