I'm about to start my undergraduate career and I'm at a loss when it comes to a solid note taking application. I use OmniOutliner Pro all the time for various tasks and love it, but I'm not sure how it would do for a full fledged note taking application.

I find VoodooPad intriguing because of it's inherent ability to crossreference wiki style. This would probably help me immensely because I tend to have a ton of random thoughts/ideas and have poor organizational-fu. However, I have doubts about it's scalability. Will it become cumbersome when I add a lot of notes?

I've briefly looked at Journler and DevonThink also and find them both to be a little overkill for my needs. I use quicksilver for file tagging and smartfolders to organize my files and I don't really need a program to do that for me.

Finally, I'm a computer science and Japanese double major. Should I keep my notes separate, or even use two separate programs?

Basically what I'm asking for are some recommendations for note-taking applications that would fit my situation (double major, poor organizational skills, tendency to explore many interesting subjects on my own). I need a repository for all of my thoughts and notes but it has to be good for inputting data also, not just for organization and searching. Any tips not related to software recommendations would also be welcome. Thanks.