I think I'll add the option to use either local MathJax or http://cdn.mathjax.org/mathjax/latest/MathJax.js available in the next update (may take a day or two) - like settings of current geogebra filter is giving 3 options to use http://www.geogebra.org/webstart/geogebra.jar (latest version), http://www.geogebra.org/webstart/3.2/geogebra.jar (version 3.2) or local applet with $CFG->wwwroot.'/filter/geogebra/32/geogebra.jar'
Geonext applet is in version 1.7.3 but I have not seen new development there during the last years so that must be the latest version of applet in lib/geonext. Sadly it's not a complete package, at least some help files are missing (for example lang_fi.jar) and when I looked at the apache error log some missing java utility file might explain this IE behaviour. I have not asket from Alfred yet.
JSXGraph files are in the latest version with one modification (commented out that debugging to enable graphs for IE9 in IE9standards mode) - if you set scripts to use the latest files for example with
<script type='text/javascript' src='http://jsxgraph.uni-bayreuth.de/distrib/jsxgraphcore.js'></script>
<script type='text/javascript' src='http://jsxgraph.uni-bayreuth.de/distrib/GeonextReader.js'></script>
some examples fail in IE9.
If sites need to use moodle offline local files are always better, if they need the latest versions external files can be all the time up-to-date but that can cause also problems for sites like http://cdn.mathjax.org/ - imagine that all moodle sites, WP sites, Drupal sites, Joomla sites... might start to use cdn mathtex some day - no server can handle such amount of http requests, it would make cdn mathjax down like sitmo latex is down now and forkosh site seems to be the only functional public mathtex site now...
For moodle sites that are not allowed to install any non-core things or change any settings or permissions (keytoschool etc) the only option to use maths might be some link to an external palette that can be attached to any forum, labels etc
For asciimathml I will most likely set those traditional 3 types of fallback scripts (in AMMathtex.php for texlive type syntax, AMMimetex.php for Mimetex/Google Chart api tex and AMMathtran.php for Mathtran/old style Tex - only AMMathtex.php is now available in my package file - and one of these files will be loaded as a part of AM.php according to selection in settings) but we could use also mathJax fallback for pure LatexMathML already without any browser detections or mathML plugins (latexmathml script must be first and then MathJax renders mathML for all browsers). So we need again more settings there to choose which options to use - in AM scripts I had 2 fallbacks AMTcgiloc (MathML in FF) and Gemcgiloc (fallback also in FF to force latex)...
In mathml I have noticed one major problem - it is easy to add math tags inside math tags and then mathjax throws errors so ideally mathml should be in editor content area in a non-editable (protected) element (img title/alt etc) and editor plugin should be a little more advanced - like moodle_emoticons plugin is showing images in editor content area but saves emoticon filter code when you press Save.