i am currently working on a web application that needs to accept video uploaded by users in any format (.avi, .mov, etc.) and convert them to flv for playing in a flash-based player.
Since the site is OpenCms-based, the best solution would be a ready-made plugin for OpenCms that allowed to upload and play videos doing the transcode operation in background, but just a set of Java classes to do the transcode would be great and then i could make the uploading form and playback part on my own.
You basically have two choices if you want to host, transcode and stream flv files (and don't want to buy a video transcoding application): you can call out to FFMpeg/MEncoder or you can use an external Web service. You could also sidestep the problem completely by allowing them to embed YouTube videos on your site.
If you go the 'local FFMpeg route' I would suggest simply using ProcessBuilder and constructing a command-line to execute FFMpeg. That way you get full control over what gets executed, you avoid JNI, which is an absolute nightmare to work with, and you keep OS-specific code out of your app. You can find FFMPeg with all the bells and whistles for pretty much any platform. There's a good chance it's already on your server.
The nice thing about the 'Local FFMPeg' route is that you don't have to pay for any extra hosting, and everything is running locally, although your hosting admin might start complaining if you're using a crazy amount of disk and CPU. There are some other StackOverflow questions that talk about some of the gotchas using FFMpeg to create flvs that you can actually play in the flash player.
The Web service route is nice because there is less setup involved. I have not used Hey!Watch but it looks promising. PandaStream is easy to set up and it works well, plus you get all your videos on S3 with no additional effort.