I am aware of following projects (mostly from http://www.w3.org/community/markdown/wiki/MarkdownImplementations):
implemented in Java:
The fantastic microbenchmark tool created by MarkdownPapers' author compares the performance for the following implementations:
TxtMark far exceeds the performance of the other tools, as shown in the following graph:
PegDown, which supports many GitHub extensions and others, is far more fully featured. Custom plugins or extensions are also possible.
My use case involved processing markdown from an administrative screen where performance was less impactful than a rich feature set, which meant PegDown won over TxtMark.