During Civil war, I know that Hulk was sent off to space, but what happens to Thor, he doesn't actually appear, only Ragnarok? What Comics should I read to follow his events, On a side not what other side storylines during the civil war, I know of The Initiative and I believe there is also a thunderbolt run, are there any more?

IIRC, Thor didn't have a comic at the time of Civil War since the previous volume ended after Disassembled. So he was in comic limbo between then and when the JMS Thor book started, after Civil War.

During Avengers Disassembled, Thor headed off Ragnarok and went into hibernation... missing, presumed dead. He stayed that way until the J Michael Straczynski run began shortly after Civil War.

-J

I believe Tony tried to get Thor to register, Thor proceeded to rip apart Tony's armor, Thor started laughing about Tony's stupidity, and then Thor goes back to Asgard. Yeah, not exactly Tony's smartest idea telling a God with probable diplomatic immunity that he needs to follow a law that can't be enforced.

The Thor/IM fight comes post Civil War. They fight in Louisiana, and Thor curb stomps IM without even trying (Thor+Runes+Odin Force). It was a pretty one sided fight in Thor vol 3, issue 3.

Thor was 'dead' during Civil War, and is rather honked off by Tony turning on his fellow heroes as well as a rather poor attempt to clone Thor.

The Odinson was at the drugstore buying some IcyHot. Because he was Thor.