We use the Java preferences in some of our apps and haven\'t really noticed this since the utility that makes the calls is fairly old and was written in Windows XP days. But
Some preferences are stored in registry keys, while some others (now I'm going to check exactly which ones) seem stored in text files; for instance, the preference "Use certificates and keys in browser keystore" is stored in C:\Users\%USER%\AppData\LocalLow\Sun\Java\Deployment\deployment.properties :
#deployment.properties
#Thu Jun 12 15:26:53 CEST 2014
deployment.security.browser.keystore.use=false
deployment.modified.timestamp=1402579613914
deployment.version=7.21
deployment.browser.path=C\:\\Program Files\\Mozilla Firefox\\firefox.exe
#Java Deployment jre's
#Thu Jun 12 15:26:53 CEST 2014
deployment.javaws.jre.0.registered=true
deployment.javaws.jre.0.platform=1.7
deployment.javaws.jre.0.osname=Windows
deployment.javaws.jre.0.path=C\:\\Program Files\\Java\\jre7\\bin\\javaw.exe
deployment.javaws.jre.0.product=1.7.0_60
deployment.javaws.jre.0.osarch=x86
deployment.javaws.jre.0.location=http\://java.sun.com/products/autodl/j2se
deployment.javaws.jre.0.enabled=true
deployment.javaws.jre.0.args=
This was verified on Windows 7 pro / 32 bit - JRE 1.7.0_60 (i586)
sources:
Related question on this site
Oracle - Java SE documentation - Deployment Configuration File and Properties
Have a nice day