3store is an RDF "triple store", written in C and backed by MySQL and Berkeley DB. It is an optimisation and port of an older triple store (WebKBC). It provides access to the RDF data via RDQL or SPARQL over HTTP, on the command line or via a C API.
Algernon is a rule-based reasoning engine written in Java. It allows forward and backward chaining across Protege knowledge bases. In addition to traversing the KB, rules can call Java functions and LISP functions (from an embedded LISP interpreter)