Now that it's been revived with Tiddlywiki5 and development's picked back up, I'm somewhat tempted to get back into it. Main advantage: Better crosslinking, rich content, etc. Main disadvantage: Less simple to edit, some tedium to export.
I'd love to have a Tiddlywiki-like frontend to a set of Markdown text documents backing it. (This is something that's been gnawing at the back of my mind long enough that I might have to buckle down and make it myself) Maybe Markdown + JSON for rich content data...