Recently went through the process of evaluating every note taking tool I could find. Settled on TiddlyWiki which is slightly unintuitive at first but very well

Recently went through the process of evaluating every note taking tool I could find. Settled on TiddlyWiki which is slightly unintuitive at first but very well thought out once you get it customized to your needs. Fulfills most of the needs I see people requesting on this thread, i.e. flat file storage, syncable via Dropbox, markdown support, wiki structure.