[ramanujan]

Omnigraffle is a lot better than this for really making pretty diagrams, because it's connection aware and can do graph layout. Also, if you learn the Keyboard Shortcuts you can be really fast. It's one of the few applications I use as much as emacs, and it's worth learning.

People in this thread have been saying pen and paper, but it's (obviously) a pain to scan a bunch of pen/paper sheets for search later or remote collaboration.

FWIW, a new solution I've been using with some success just over the past few days is Penultimate, a really simple/nice IPad notebook app -- as distinct from a sketching app.

http://ipad.maccreate.com/2010/04/16/penultimate-ipad-app/

Use that with a $15 Pogo Sketch (you can get it in the Apple Store) and a $11 pair of fingerless cloth gloves from Hot Topic (http://www.hottopic.com/hottopic/Accessories/GlovesArmwarmer...)

The gloves are really handy as they turn off palm detection, so you can rest your hand on the Ipad surface while you use the stylus, just like a normal sheet of paper.

[tvon]

I'm far too entertained by the fingerless gloves. Clever setup, though.