Jena (http://jena.sourceforge.net/) is the most widely-used at the moment, and relies heavily on community standards (OWL, SPARQL, etc). Other options are:
KOAN (http://kaon.semanticweb.org/), which perhaps can be used in a more scaled-down fashion, but strays from pure standards with some proprietary language and extensions.
Sesame (http://www.openrdf.org/), which you will find comparable to Jena unless you are interested in comparing large-scale triple retrieval efficiencies, or you need to support OWL.
JRDF (http://jrdf.sourceforge.net/), supposedly blending several of the RDF frameworks, but I can't say I know anything about it.
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