Some nightbuses
Prague to Lyon, via Munich with Flixbus. About 50eur, 18 hours, a couple of hours to wait in Munich (time for a pretzel and a coffee). Munich ZOB has a Lidl, and a dm, some restaurants, luggage lockers and isn't far from town. Downside: the toilets are 50c, and grim.
There's a much cheaper direct bus from Prague to Lyon with Regiojet, which I originally thought I'd be taking when I decided to go from Prague. But it has limited departures, and I would have arrived a day earlier than I wanted, so I went with Flix.
The journey itself (the night part, Munich to Lyon) was pretty awful. Constant interruptions by the police, mostly in Switzerland. They came to passport check at every stop and sometimes in between. The two black guys on the bus always seemed to be singled out for a bag search when nobody else was. The bus driver had yelling fights with two different sets of passengers, both a couple with a small child. The first, brought too much luggage and he wouldn't let them on the bus. They were yelling a lot outside the bus, which was audible inside, making lots of phonecalls, and eventually the Swiss police turned up anyway. The bus was delayed about 45 minutes, and the family did not board. The second time a family hadn't been woken up at Zurich and were upset to find themselves in Lausanne. Dad was yelling in French, Mum was begging the driver to speak English, and driver only wanted to make demands in German. Some passengers tried to help, but of course the Swiss police were already here. The driver wanted to charge them for their 'illegal' ride from Zurich to Lausanne. Srsly.
The return Lyon to Munich with Flixbus was 30eur, 12 hours; same driver, but no yelling this time. I had two seats to myself, and mostly slept. Still interrupted by Swiss police a lot, one time with a cute dog who sniffed everything.
After a day in Munich, I took Munich to Krakow; 13 hours, 40eur, Flixbus again. After Regensburg I again had two seats to myself, and slept pretty well. We were entirely uninterrupted by police or passport checks; we went through Austria and Czech Republic, and all borders passed unnoticed.