Traveling the Balkans:

John,

You might try also posting this question on the Lonely Planet Thorn Tree forum as the group there has lots of experience with some of the "lesser travelled" parts of Europe. I suspect you'll find that trains will be the best method on some routes and buses will be the only method on others. You'll need to have a specific list of the cities you'll be visiting before deciding on the best transportation method.

Are you planning on doing any hiking, especially in Serbia or Kosovo?

John, I am going in September, and I have found there are no trains going into Albania. The Belgrade to Bar route has only one overnight train right now and takes over 9 hours. Anything you have found and can share with me also appreciated. I am also doing Montenegro, W. Bulgaria, Bosnia. Skipping Romania, Hungary.

I would do that planning using the latest edition guidebooks from Lonely Planet, which will certainly include some bus summaries, or perhaps Brandt. You'll also need to reconfirm schedules locally as you travel. Buses likely will serve more destinations in some countries, although trains are perfectly easy to/from/in much of Hungary, for instance. Albania does not have any international train connection, only a couple of lines within its own borders. How to Look Up Train Schedules Online gives you the DB train schedule link, which works for all of Europe. You cannot easily rent a car to take to all of these countries.