The classic recommendation would be Passau - Vienna as the infrastructure is very well built out and Vienna is a great destination. This can easily be combined with a start in Munich and taking the bike back on the train to Munich for a round- trip that takes around 5-7 days (+-500 km).

That being said a few other sections come to mind:

- the very start from Donaueschingen to Regensburg is on beautifully wild cycling paths in the middle of nature with a number of interesting cities along the way

- Vienna - Budapest + train back is another fun loop including 3 capitals!

- For the more adventurous, the Serbian part is very scenic too. Belgrade is great. Leaving it on the busy road not so much. After that you quickly find yourself on a meandering road along the shore with spectacular cliffs and tunnels. No cycling path anymore. But well worth it.

- Romania is still challenging for cyclists, but the delta is very spectacular if you get a chance to visit it (by boat, no bike , as there are no roads).