I use Emacs with org-mode, while I don't know how it handles searching (there are commands for searching tags, I haven't used them). My notes evolved into unmaintainable mess, except for periodically cleared parts like homework to-do list (removed after finishing courses).
I've written a personal wiki implementation [0] for such uses, while it's not ready yet. It has a Web interface, data in text files in a git repo, tags, fulltext search, binary attachments/images, BibTeX metadata export, browser bookmarks import. (It's designed for running on a local machine, not an external server.) Some of the main reasons why I don't use it is that it has no Emacs integration and that my workflow for sharing data between my computers depends on Mercurial bundles, while it supports only git. [0] http://lethe.mtjm.eu/
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