I was being semi-productive on my Windows virtual machine when I was faced with this:
No way to say restart later, no way to cancel it. WHY? I hope this has changed in Windows 7 because this is terrible UI flow. I'm not sure because I have yet to get all the software I need to run on Windows 7, but I'm sure that day is coming.
This goes for web applications, desktop applications, and operating systems, as well as Java applications. Do NOT steal user input control, do not change user input. The more you attempt to "help" a user by doing something for them, the more likely you are to drive the user away.
My host system, Kubuntu, doesn't do that with the exception of the Groupwise client. I am far, far more productive with native software on my worst day using Linux than on my best day using Windows.