For a straight sci-fi show, there was a lot of romance and all of the main characters had their own happily ever afters (including two AI's--a robot and the aforementioned smart house). While I shipped pretty much all of them (yes, including Andy and SARAH), my favorite couples were the two that had the most difficulties--Jo and Zane and Henry and Grace. Both couples were thrown for a few loops in the last couple of seasons and managed to survive all of them. That's probably why I liked them so much.
Jo and Zane
These two never seemed to be on the same page, which made their romance complicated to say the least. They first got together in the 2nd season and were running towards (and away from) each other from his very first episode (E=MC?). When it finally seemed as if they were going to be together for good, Jo got wormholed into 1947 (along with Jack, Alison, Fargo, and Henry) and after returning to the present she found herself in an alternate time line in which she and Zane never got together. For the first part of season 4, she tried to get over the Zane she knew as he dated Jack's daughter, but by the beginning of season 4.5 things started to look up for them after Zane found out about the original timeline. Their relationship was still a bit bumpy right until the end of the series, it was much more stable than the one they had before the change-up.
What I really liked about this pairing was that they should not have worked. Jo was Ms. Law and Order and Zane was a felon with an immature streak a mile wide. However, they just sizzled and brought out the best in each other--in any timeline.
Henry and Grace
After returning from 1947, Henry found himself with a wife he didn't know and had only met once before going through the wormhole. Grace had no idea what was wrong with the man she'd been married to for years, but she knew something was up. She just didn't know how to fix it. What made them such a fun couple was watching Henry fall in love with this woman he never would have imagined himself with--and even serenading her with She Blinded Me with Science to win her over.
The video I chose for today (not the one I wanted, but I couldn't find that one anywhere) is from the show's series finale and shows all of the couples with their HEA's. The song is You Are My Home and I love it because that's exactly what all of the characters found in the end--all because of the 1947 wormhole. I'm sure many fans complained like hell when season 4 began (I know I was pissed when I started watching it), but I think it was the perfect way to further the storyline. By putting five characters into situations they never would have been in if they stayed in the original timeline, they were able to grow into a family. They may have all known and respected each other in the first few seasons, but characters who would never have been friends found themselves becoming just that (Fargo and Jo and Fargo and Zane, especially). That's what made it so sad when the show ended.