'The chamber of understanding' is first seen in season 6, episode 2 of Futurama titled "In-A-Gadda-Da-Leela". It is a chamber that the character Professor Farnsworth uses when he needs to, surprisingly, understand things. The chamber itself drops down from the ceiling and plays disco music, complete with disco ball.

I'm unsure of the actual origins of the meme itself (help would be appreciated) but a forum thread was started here, a few weeks after the episode aired, with reference to it: http://panelsonpages2009.forumotion.com/t4187-the-chamber-of-understanding

The meme is used on the internet as a response to posts or topics and shows that the person is considering or trying to understand the topic or post in question.
There are several variants of the meme where the disco music is replaced with a different kind of music or song. For example the music is replaced with Rick Astley's 'Never gonna give you up'

Original: https://www.youtube.com/watch?v=VCcOXVA7ABA
Rick Astley version: https://www.youtube.com/watch?v=U_qAwSnGCo8&feature=related
The chamber of the kraken (metal): https://www.youtube.com/watch?v=LO1Qr4Pyu_E&feature=related

Several single serving websites have also appeared around the internet. examples as follows:

http://chamberofunderstanding.ytmnd.com/
http://chamberofunderstanding.com/

(please note this is my first entry to KYM, I know the article quality probably needs work, any help would be appreciated in finding the exact origins, the spread of it and help with cleaning up the article, thanks)