It is possible to access bits of MATLAB\'s internal java code to programmatically change MATLAB itself. For example, you can programmatically open a document in the editor
To find out more about java objects, I use uiinspect.
The only place I know that is documenting the Matlab hidden Java stuff is Undocumented Matlab by Yair Altman. His site lists plenty of very useful tricks. Being able to use Java to format text in list boxes has come in very handy for me, for example.
EDIT
The man has spoken. Listen to him, since I don't think there's anyone outside MathWorks who knows more about Matlab's internal java code.