Just to 'get ze Ball rolling' on great German modern movies:
"Lola Rennt" http://www.imdb.com/title/tt0130827/
"Good Bye Lenin!" http://www.imdb.com/title/tt0301357/
"Im Juli" http://www.imdb.com/title/tt0177858/
"Das Leben der Anderen" http://www.imdb.com/title/tt0405094/
- and looking very much forward to other input! :-)
I would highly recommend other Fatih Akin movies, namely "Head-On" and "The Edge of Heaven". If you have not seen them already that is. Also:
Antibodies
Revanche
The Princess and the Warrior
Gloomy Sunday
I am not sure if you were only asking for German comedies, but I will go ahead and contribute ones I highly recommend, ranging from very good to that of damn-near masterpiece.
The Nasty Girl (1990) Comedy/Drama that drags a little towards the end but just try to get through it.
Mostly Martha (2001) Romantic comedy with good laughs and a mindblowing kiss scene.
Sophie Scholl, The Final Days (2005) Drama based on historical courageous figure.
Das Boot (1980) Cult film classic based on WWII events.
DownFall (2005) Great film detailing the last days of Hitler.
Cherry Blossoms (2008) This one is a tearjerker with it’s bittersweet ending.
Nowhere in Africa (2001) My choice of being almost a solid masterpiece. Warning: film contains explicit realistic love scenes, which may offend some. It didn't me!
Enjoy!