Java has a lot of dependencies and would fill up your flash drive. There is however something called a 'chroot jail' which is like a mini virtual environment that you can create in a folder on your NAS. After you set it up and 'boot' it, you can install apps in it and it runs in parrallel with FreeNAS. I'm adding the finishing touches on a HowTo for using JDownloader which uses Java and would be perfect for what you want to do. I used to be an avid Tivo fan but switched to MythTV and haven't looked back. Here's a link to my HowTo, I'm still trying to clarify details. I'll try to help you if you have questions about it, but I'm spread a little thin right now, so see what you can work out on your own if you can.