What's the meaning behind all the chairs in Madoka's room?
Those chairs are a direct reference to Bokurano, understanding which actually adds depth to the scene (if you've seen Bokurano).

Bokurano huge spoilers:


   Childs sitting on the chairs are actually giving up their lives for the privilege of fighting a defence of Earth.
 Note that chairs appear before the big reveal about souls and zombies in Madoka.