Do you know any open source tools or libraries (preferably Java, but that\'s not a strict requirement) in the GNU/Linux world that convert mathematical equations in LaTeX syntax
You may want to have a look at LaTeXML. It converts LaTeX to various XML formats, including OpenMath and content MathML.
But be warned, like all other tools, the conversion from (presentation-oriented) LaTeX to content markup (as in OpenMath and MathML) is heuristic. In particular, in ambiguous situations (e.g. $f(a+b)$, which can mean $f$ applied to $(a+b)$ or $f$ times $(a+b)$) LaTeXML chooses one (usually times).
There are two ways out:
1) use content markup already in the LaTeX source (see http://trac.kwarc.info/sTeX)
2) use a better post-processor for LaTeXML is working on this