I did some familiar wiki hopping today. WikiMatrix is a very good place to go to if you wish to compare the plethora of offerings out there. Another site is OpenSourceCMS where you can very conveniently use the demo installations of practically every free/oss cms/wiki available.
As for my top wiki's (in no particular order) dokuwiki, moinmoin, twiki, (i have used these three) and pukiwiki, pmwiki and oddmuse dokuwiki in particular is being used a lot in our computer science department.
these stand out because they are foss, have file based backends, have flexible markup, infinite features, will run on any web-server with php and are under active development. check out the link in the title to see a list of features.