Because it ships by default with Ubuntu, I've been using Tomboy for my occasional note-taking needs. It's convenient and all, but it's a little too heavy with its Mono requirements. No problem for my desktop, but I wouldn't install it on my stripped-down laptop.
A more lightweight replacement for Tomboy is Zim. Like Tomboy, it's a desktop wiki in that you can automatically create links within notes. Largely, though, it feels like a much improved notepad.
Zim works like Tomboy in almost every way. Possibly the only thing it lacks is the synchronization feature. But I don't use that anyway.
Here are the things I like about Zim over Tomboy:
it's a lighter program without heavy dependencies
documents are stored in plain text (with minor markups) in easily accessible directories, making it easier to back up
much improved document formatting, including embedding of pictures
word count tool
intuitive and accessible organization
Overall, it feels like a good mix of Tomboy and Gedit.
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