My instincts have always told me it has to do with Snape. Snape convinced Voldemort that there was some profit in keeping Lily alive. Perhaps Voldemort had decided that Imperius would be the way to get what he wanted from Lily, since she had made clear that she would not acquiesce to his demands otherwise. If, as HPSpec suggests, he attempted to Imperio her away from Harry and failed, perhaps it became clear to him that he would never be able to control her, so he finally killed her.

It is complete speculation, but I cannot help but think that this has something to do with Potions. I suspect that we were not given all of that wistful reminiscence of Slughorn's for nothing. Beyond that, I am so far out on a limb that there is no point in more speculation. If anyone has a clearer picture, by all means, post it on the forums and let us discuss.