You can use SWOOP also.
Yes, Protege is the most widespread tool, I guess, but I personally do not like it, at least you should find the version you like most, because in its case the last doens't mean the best.While I was working at STI, I was using their ontology modelling tool - WSMT. It is open-source, http://www.sourceforge.net/projects/wsmt
It allows to model in several ontology languages(WSML, OWL) and use several reasoners. Moreover, it allows to visualize the ontology. With Protege it was a bit difficult. Here is nore information about WSMT and some tutorials: http://wiki.sti2.at/index.php?title=WSMT_Tutorials
One (if not the first ) tool to give a try is Protégé http://protege.stanford.edu/
with quite some history (implying a certain maturity level) and authored by knowledgable folks at stanford university.
It is free, open source, in java, supports various representation formats (like frames, OWL, RDF). it provides means for extensibility, which is alredy used by quite a few plugins (eg for visualizing, reasoning).