For me, "just a bunch of txt files" here. They're as electronically portable as it gets, easily grep-ed, and easy to deal with using Perl ;-)
If you're having organizational issues with txt files, spend some time at creating a directory structure that is mnemonically accessible to you. A two-level directory structure (organizing the txt files by topic keyword) can do wonders for your txt files.
You can use minimal markup to power your txt files into different formats using
reStructuredText. There is a
Vim script that could help.