I quite like FreeMind for taking notes - it's a mind map application.
You can create bubbles for each topic, and put detailed notes in each, decorate the bubbles with icons, and break large clusters out into their own linked files.
FreeMind is written in Java and will work on Windows and OSX as well.
For more prosaic note taking I often find myself using a TiddlyWiki - this isn't an Ubuntu app per-se, it's just an HTML page with some clever JavaScript embedded in it. You can take notes and link between topics easily, much like Tomboy. I have an empty TiddlyWiki in my templates directory so that I can create a new one with a right-mouse click any time.
Both these approaches work well on any major operating system - and TiddlyWiki doesn't even need you to install anything.