It just became an append-only log for me with very limited organizational power. Though I do like it for anything just long enough where a single .txt file doesn't cut it. Tiddly is great for that case because it encapsulates the common task of jumping between the same sections over and over -- the real downside of a large file. But you aren't alone in finding it's not so great on a larger scale.

So if you did like the idea of a wiki but weren't diddly with the Tiddly, might be worthwhile to check out something like DokuWiki or MediaWiki.