Cersei Lannister may have been a hated character from the start of Game of Thrones, and with good reason, but she had her reasons. Cersei was horribly limited by her gender, ditched by the man she thought she would marry (for another woman), and then forced into a loveless marriage with a King who was actually a pretty terrible husband.
Robert Baratheon may have been a great warrior once, but he was not a great King (and would rather hunt and drink than rule), and was terrible to Cersei, too. He made it clear that he would also have rather been with Lyanna Stark, largely ignored Cersei to go and do the hunting and drinking, made no secret of his brothel visits, and even hit her. Perhaps if Cersei had been with someone that better matched her, she might not have ended up as quite so much of an Evil Queen.
Ned Stark
This may seem like a completely insane suggestion, as Ned and Cersei hated each other in the show, but they may actually have made a solid pair. Ned's morals and devotion to honor could have tempered Cersei, and as he would have been a more active ruler and someone who respected women, he may have given her the kind of power and voice that she craved. She would also have pushed him to become stronger, and occasionally to play the game in a way that wouldn't end up with him being beheaded - not to mention that he would have made sure their children were not raised to become Joffrey!
Rhaegar Targaryen
This may be the most obvious choice, but it needs to be said. Had Rhaegar not jilted Cersei for Lyanna Stark, and simply allowed their marriage to go ahead as planned, a whole lot of disaster would have been averted. The wars against the Targargyens wouldn't have started, Rhaegar and Cersei could have taken the throne from the Mad King, and while these two may not have been the best pairing, it's likely that Cersei wouldn't have been anywhere near as bitter about her lot if she had actually felt loved.
Jaime Lannister
Arguably, these two were together - that is, they were together enough to have multiple children! And of course, this wouldn't be a political match - or even an appropriate one, seeing as they are siblings.
However, had Cersei and Jaime run away together (perhaps to Dorne, where incest is apparently a completely normal thing), they could have simply lived out their lives together in peace with their children. It's not something that works for the realm, but then again, neither did keeping them apart.
Stannis Baratheon
Stannis and Cersei would have been a serious potential power couple, especially if the two had married after Robert's death. Stannis' wife was clearly not the best choice for him - she's a religious fanatic, a terrible mother, and obsessed with having children. In many ways, Stannis' wife is his downfall, especially as she brought Melisandre to them. Instead, Stannis with a strong and practical wife like Cersei could have been a fantastic king.
Ellaria Sand
These two definitely didn't like each other very much, but they would have made a surprisingly impressive power couple. For one thing, Ellaria's Dornish sentiments would mean that Cersei's relationship with her brother (and anyone else she felt like bedding) would be totally acceptable. For another, these two are cunning, ruthless women, sick of being behind the scenes. Together, these two could out-manipulate anyone, and would have no compunction about taking out anyone in their way. It would be a terrifying union, but a seriously powerful one.
Littlefinger
Cersei may be hungry for power, but if Game of Thrones proves anything, it's that she doesn't actually really have the temperament to rule effectively. However, she could do very well with another power-hungry character who could scheme away with her behind the scenes (and keep her from getting too terrifyingly close to the actual throne). Being able to play with the rich and powerful, lording it over the women of the court, enjoying wealth, and generally doing what she does best - without having to be married to a boorish King? Littlefinger could suit Cersei very well, and they would be a good match for each other.
Doran Martell
Doran Martell was a bit of a disappointment to many book fans in the show, and had the potential to do so much more... and if he had married Cersei, that may well have happened. The ruler of Dorne would have been an appropriate match for Cersei in of social standing, and these two would likely have balanced each other out well.
Cersei could have galvanized him to do a little more, and Doran would have provided a good calming presence for her ambition. (And, as with Ellaria, there would be no issues with her relationship with Jaime).
Melisandre
This may not be the most romantic of relationships, but Cersei and Melisandre would have made quite the power couple. Of course, had Cersei not married a man in power, then she wouldn't have been able to stay in the court and in the ranks of the powerful the way that she would want. However, Melisandre clearly made her way into the highest echelons of society, and there's little doubt that Cersei would have been able to, as well. Combine their ambitions, lack of morals, and interest in magic, and you've got an interesting (and dangerous) combination.
Jorah Mormont
Jorah doesn't have the best luck with women, sadly, but Cersei may have been a decent match. His first wife, Lynesse, nearly bankrupted him and drove him to slavery in order to fund her lavish lifestyle, and then Daenerys refused to truly return his love, despite his devotion. Jorah is an interesting character - honorable, but with a seriously dishonorable past. He could have been the perfect balance for Cersei, someone who is intelligent and morally flexible enough to work with her, who respects women, but who has honor enough to keep her worst impulses in check. And of course, given the house that she comes from, Cersei wouldn't have pushed him to criminal enterprises to her.
Herself
This may be cheating a little, but in all truth, Cersei shouldn't have needed a husband at all. Some of her biggest issues came from struggling against the fact that no one would allow her any power on her own, that despite being arguably the best choice as heir to Casterly Rock, she could never take her family seat. She was permanently under the thumb of other men, and it was a large part of what pushed her to such extremes. Had she been able to simply live her life independently, she would have done far, far better.