I've identified 6 modules that should be modified to avoid AccessControlException's while running within an Applet. My solution would be to catch each AccessControlException and then use a default or continue on. For most of these, that is probably the best solution, for a few especially PDFStreamEngine someone may have a better idea.
The modules that have issues:
pdfbox\pdfparser\BaseParser – line 131 call to Boolean.getBoolean, line 170 call to Integer.getInteger
pdfbox\util\PDFTextStripper – line 79 call to System.getProperty()
pdfbox\util\ResourceLoader – line 67 call to getSystemClassLoader()
pdfbox\pdmodel\graphics\color\PDColorState – line 50, call to Color.getColor
pdfbox/encoding/Encoding – line 78, call to System.getProperty
pdfbox\util\PDFStreamEngine – Line 351 & 364 check for font == null (will be null if had resource loading problems)
Not sure what the best way is to proceed. Please advise.