With the Illuminati and all throughout the Civil War story, Stark was pro-registration.
Why then in the Spider-Man issue (included in Road to Civil War) did Tony go before congress to argue against it?

@velcro108: I think Tony was originally against it but Marvel decided to change that later after the Stamford explosion. I'm pretty sure Stamford take place after that Spider-Man issue.

Understood, but in that Spider-Man issue, Tony even referenced his meeting with the Illuminati in which he was trying to talk them into supporting it. Richards and Black Bolt agreed with Stark. Dr. Strange got pissed and left the meeting and Namor didn't care because he felt it wouldn't effect Atlantis.

In Illuminati, Stark says of the Registration Act: "We should happily come out in favor of it." Then in Spider-Man, he refers to it as "The enemy." This is both before Stamford. I understand why he was initially for it (he explains that clearly in Illuminati). But it is never explained why he later argues against it in D.C. with Peter Parker by his side.

Not really flip flop, its just that I don't think Tony Stark ever wanted the Registration Act to be passed. It was the enemy of the traditional way that superheroes did business, however he also notes that he see's it as inevitable that it will be passed. Which is important, because there's not much that he or any other hero can do to stop it. However, he does attempt to slow it down. Once you have the Stamford incident however it is what it is, and he basically says that "It's the law and I think that if its going to be the law we should just go with it, instead of trying to fight against it".

Or he was just plain lying.

Actually I think he isn't flip flopping, because there is an issue where he tells the Illuminate that the registration act was coming and that it would pass. He argued that he and the others should come out in favor of it simply to curb it before it was made really though on them. The result was that only Reed thought it was a good idea, with Namor having just left without concern, Black Bolt making some gesture (probably telling them not to bother with bringing it to Attillan) and Strange leaving with a notice of never calling on him again.

Stamford ofc just brought it out all the quicker and Stark, as director of Shield led the charge, all in order to avoid someone like Osborn or Maria Hill getting the job.