I got curious over the whole "Lain is universal" claim a while back as well and tried asking for answers on the OBD, but didn't get much help in that area.
Being a Lain fan myself, my thoughts are that her abilities to warp reality are only on a planetary scale based on her connection to the wired world on Earth. There is misassumption by some folks that anyone who is a reality warper is capable of warping anything in the universe to their whim, yet there have been cases in fiction where reality warpers have limits to what they can manipulate or how far they can extend their influence like Tsukihime's Arcueid or characters with a personal dimension they can control like D Gray Man's Road Kamelot and Marvel Comics' Blackheart and his Darkforce Dimension.
@Dream: You used to have Lain as an avatar, so I guessed you where a fan. So she's probably a planet level reality warper? Though to turn back time on Earth wouldn't that effect at least the Sun too? I haven't seen the series so I can't say really. Even if she was only planet level I'd say she still beats Haruhi Suzumiya as Haruhi has no control over her powers and Lain does, though I think Haruhi has been shown to be universal.
Disregarding what I said above, I would say there are at least two levels of reality warping; universal and multiversial.