Uh, not in #500, that was during Stark Disassembled... Surprisingly, that part was handled really tastefully and was actually very good and in-line with the little chracterization that there was. Both of them were going on the run from Osborn and on separate missions where they could very possibly die and were basically about the only people they had left at the end when everything they had, had been taken away. (I mean, there was Pepper but she wasn't on the run yet) So they had a sort-of mutual pity/maybe the last time ever-fuck in a very desperation fueled move...

It was the Tony/Pepper which happened shortly afterwards which was *puke*... As has already been stated above, Tony was in a BAAAAD place and very very unclear with what he remembered or not and Pepper basically jumped him. (Yes, that is not an exaggeration, Tony was not fully capable of informed consent at this time, while Pepper whatever her emotional state, *was*)