"Clunk" represents the sound of something metallic falling into place. It's comparing the brain to a machine suddenly slipping into gear. There is a colloquial expression "the penny dropped" which means the same thing: a sudden realisation.

"Knight met James O'Keefe two and a half years ago and she's in love. The couple live in north London and Knight says meeting him was when her brain went "clunk". "Before that, there was no clunk," she says, and laughs."
http://www.scotsman.com/lifestyle/interview-beverley-knight-...

This means that when she saw him she realised he was the man for her, something that had not happened to her before.

"Just saw you post this here and I was like wuhhhh? Why is she posting this? Then I read the last line again and my brain went clunk."
https://community.sephora.com/t5/Besides-Beauty/The-Disney-T...

This is about an apparently pointless post with a pun in the last line, and when you notice the pun you suddently understand the point of the post.

"Something in my brain went CLUNK! That phrase was very familiar to me. Suddenly all the names registered"
http://recogitare.com/MyBB/showthread.php?tid=162&page=7