I use OmniOutliner to store all my uni notes. I love it. I need not say more!
Snow Leopard has a lovely substitutions feature (smart quotes, dashes, text substitution and
data collectors). It's very efficient (particularly when you're speed-typing during a lecture) and integrates automatically with Pages.
Currently, you can turn on text substitutions in OmniOutliner manually (right-click). But they turn off after the document is closed. You can force text substitutions to stay on for all Cocoa applications with a
defaults tweak. OmniOutliner doesn't respect this either (this may be purposeful by Apple to ensure old apps don't break; developers have to manually approve this in their app.)
Please support all substitutions in the next update.