It'll probably be a long time before Gilmore Girls fans recover from those last four words that were uttered at the end of the series. While some may guessed that the show would end with Rory saying she was pregnant, it seems most fans didn't think the father of Rory's baby would be a mystery and some still don't. In fact, many fans believe that Logan is the father of Rory's baby but is he?
Although fans knew all of Rory's exes would be in the revival, it was unclear just how frequently each one would appear and Logan definitely got the most screen time out of all of them. In the first episode, "Winter," viewers found out that Rory and Logan were having an affair. Although Rory was dating Paul — who was often forgotten by everyone including Rory herself — and Logan was engaged to a woman named Odette who lived in Paris, when Rory would go to London the two would hook up. They had a "what happens in Vegas, stays in Vegas" agreement, so while they were together they were together, but once they were apart their relationship was over.
This set up worked for while until Odette moved in with Logan and Rory decided to end things completely. However, not wanting to end on bad terms, Logan came to Stars Hollow with the Life & Death Brigade to surprise Rory with one last night of fun. The two slept together one last time and then parted ways. This last hook up probably would've been the conception night of Rory's baby, however, as some fans point out, Logan wasn't the only person Rory hooked up with in the revival.
In the second episode of the revival, "Spring," Rory had a one night stand with a Wookiee. It was her first, and probably last, one night stand and Rory didn't even seem to know the guy's name. However, it seems doubtful this is the father of Rory's baby because when Rory told Lorelai she's pregnant at the end of "Fall," she doesn't even appear to be showing yet, so it seems much more likely that Logan is the baby daddy since the last time they were together happened at the start of "Fall."
From what viewers saw, Logan and the Wookiee are the only possible options for the father of Rory's child. It seems very unlikely that she would've hooked up with Paul since he never appeared again after "Winter" and Rory didn't seem all that affected when he finally broke up with her. She didn't even seem to be interested in Jess (romantically at least) when he showed up in Stars Hollow. So the most likely option is Logan and it would be very surprising (and disappointing) if it was anyone else. Logan has always been thought of a parallel to Christopher and making him the father really would bring this story around full circle.