wiki's tend to grow into undifferentiated masses with lots of duplication everywhere. One approach is to simply give up on structuring your data, cut your data into small, cohesive docs as best you can (40-80 words), throw into database and index with sphinx, SOLR or elastic Search.

Alternatively, searching for better tools/software: this guy's topic map blog is good (but prolific): http://tm.durusau.net/