The official line is that he wanted to take "a break" from the show.

Michael Shanks was asked this question at San Diego Comic-Con International 2004.

When Michael was asked why he left the series in season 6 he joked, "Because I hate Rob Cooper." After the laughter died down he followed with the more serious response of, "I needed to take a break from the show. I had a really good year off and then we decided to work together again, it was as simple as that. Nobody expected the show to go on so long and we had options in season 7 and now season 8, and who knows after that."

There was also the suggestion that he was unsatisfied with his character's writing in the prior season.

Shanks also believes that what he says and what gets into the media for his fans to read are two different things. "I read something that claimed I said I hated writers and denigrated their talents. That wasn't it at all! It was never my intention to insult them. I thought the writing staff was just great and did a marvelous job. In a way, maybe I wanted to stay on the show, but I just expressed that the character (of Daniel) wasn't being made use of as well or as creatively as he could have been. I had begun to think the show would work just as well without me and that's when I felt that I had to go. I also felt it was time to expand my horizons and look to other things as an actor." "The writers disagreed with my point of view. I thought they didn't see what I was talking about. I realize now that I should have left it at that. We had artistic differences, which is what a lot of actors say, but I hated the public speculation that would create. I wanted to be more specific, and it just seemed to cause more hurt feelings. So now I wish I could go back and say we had artistic differences and that's why I left. There is no right answer, given that situation." Shanks pauses. "But," he says pensively. "I am learning to curb what I say."

There's a hint that there were "financial reasons" for his return (e.g. he was offered a chunky pay increase by MGM, possibly coupled with the fact that hadn't been able to find much work over the course of the previous year)