I used Zim-wiki for years, and loved it. However, there is a fatal flaw in Zim that people using it for notes about code should know about. Zim parses all text as "wiki text" and some computer code snippets get parsed and interpreted as formatting. See this bug: https://bugs.launchpad.net/zim/+bug/585300

Other than that issue, Zim is brilliant. The developer is very responsive to most issues and feature requests. Sadly, Zim wasn't for me as many of my notes involve code.