Sweble is probably the best Java parser of wikitext. It claims to be 100% compliant with wikitext, but I seriously doubt that. It parses wikitext into an abstract syntax tree that you then have to do something with (like convert it to HTML).
There is a page on mediawiki.org that lists wikitext parsers in various programming languages. I don't think any of them do 99+% of wikitext though. In general parsing wikitext is a really complex problem. Wikitext isn't even formally defined anywhere outside of the MediaWiki parser itself.
