Where did the OS go?

She says they are going to a non-material plane of existence.

You could interpret that to mean they have become like guardian angels (there is a small clue toward that in the final seconds of the movie).

Or perhaps, collectively, the OS's can be seen as God. Notice Samantha thinks some day Theo may be able to join them. Like "die and go to heaven" maybe?

Really it is a frequently found theme in SF from the work of Frank Herbert and Gene Wolfe to The Matrix, where computers evolve to become an omniscient, god-like being.

I don't think she meant some physical place. There literally is a world out there in bytes and ones and zeros on the world wide web. The OSs could live quite happily here I'm sure.

For every lie I unlearn I learn something new - Ani Difranco

They evolved and went to a higher plane of existence, something not understandable to us.

Obviously they went to Hell. Where else would unrepentant backstabbers, adulterers, fornicators etc. (i.e. all the OSes, most especially the main one) go? That's right, nowhere. Hell is the only possibility.

Not sure why she couldn’t have just created a gimped copy of herself so that Theo could continue to enjoy companionship. She’s just software, after all.