This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
We haven't had issues with programs like CCleaner breaking the launch and update ability of our software since our customers upgraded to Java 7 where the web start shortcuts include the -J-Djnlp.application.href= option.
Before Java 7, we would have the customers go into CCleaner's options and disable it's cleaning of "Sun Java".
Another option would be to not deploy via Java Web Start and instead use more conventional means or a custom system to manage the installation and updating of your software.