Jesse,
TiddlyWIki is possibly one of the best tools for knowledge base design, however it really depends on the end use. Need it be read only or update for most users, need it me multi-user update, how big could it get, do you want to share it in a single file, or host it on a server.
Try and give us a brief but comprehensive outline of your Knowledge Base so we can advise better.
Google is you friend, add Tiddlywiki to any search and you will often find answers there, often referencing the forum I may add.
Regards
Tony