What are you currently using to search? You should be able to find the full schedules on www.csa.cz/en, the CSA website.

I'd agree with the earlier poster that you probably want more than 2-3 days for Berlin, so if you're still taking alternate suggestions (Can't believe I'm following in your footsteps here, GU! ), what about Vilnius, Riga, or Tallin? I believe CSA has direct flights to all three of the Baltic capitals, they're short flights, and each are interesting and somewhat off the usual path cities that would be a great fit for a 2-3 day window.