HotEqn is an app I found on the web by surfing for "LaTex and Java", and it seems relevant. It parses LaTex code and displays it in an
applet window. LaTex is, of course, the typesetting language for mathematicians, but it would work for chemists as well. The applet source code is available.
Maybe MathML is something to look into also, it's a way of viewing equations on the internet.
Chris