Which Bank for salary account

You can check online comparison webpages like this one:
    https://girokonto.focus.de/
However, more and more banks are introducing (sometimes hidden) charges, because due to the extremely low interest rates their other streams of income dried up.

You could open an account with a credit union (for example Volksbank, Sparda Bank, Raiffeisen Bank).
These institutions are owned by the collective of all customers. Once per year all customers/owners would be summoned to vote democratically on all important decisions (such as account fees).
Therefore, these banks don't have a general manager who earns a million euro per year, and on the other hand, salary accounts are usually free. (And if not, then that's the customers' own decision).

Thank you for the info @Beppi, @Janrohn 

Contrary to JanKrohn above, I found the collectively owned banks (like Volksbanken) offering neither lower fees nor good service. Due to the consensus-based approach, they are slow, conservative and old-fashioned. However, they have many branches (while the other banks move online and close offline presence) and are probably best if you want to speak to someone over the counter.