1) How do I make my DVDs appear?
2) Is there any way I can apply a filename filter to the files that are scanned to stop the thumbnails appearing? (At the moment it's still Flickr, but I want to put family pics there eventually.)
3) How do I stop the "Empty" media server appearing? I'd also like to rename the working one from Media Tomb to something more family-friendly
1) UPNP will only work with 'media' files. The DVDs are disc images which are not understood by upnp systems. To do this you need to rip your DVDs not as images but as media files with an application like 'makemkv'. You would keep the movie and chapter locations but lose all the dvd menus and special features.
2) The mediatomb documentation has a mechanism for you to define all the valid file extensions for known valid file types and then to tell it to not import any 'unknown' file extensions. This sounds like you can define the valid file types and omit '.tnj' as a valid extension and it would omit those files completely. The mediatomb docs are here: http://mediatomb.cc/pages/documentation#id2536421
look about 2/3 of the way down the page in the <mappings> section.
3) Hmm, I've not seen this myself so I'm not sure where it's coming from. Ah... Mythtv has an internal UPNP server ... it's likely that both are showing as both are valid upnp servers.
Another thing to keep in mind is that the ps3 has very specific container/media-format combinations which it will play. Media that does not conform will not play properly, you can set up mediatomb to transcode these files on-the-fly into a format the ps3 can play.