Let's see, these are the strange, obscure ships I like at the moment.
Minerva McGonagall/Tom Riddle = I just like the idea. It adds a little humanity to Riddle and vulnerability to McGonagall. Do I think JKR will go for it? Probably not, so it is a fan pairing.
Jo/Laurie = I will go to my grave swearing that Alcott made a mistake, ruined her book and gave us dreary sequels. Most pals I talk to agree it should have been this pair. But Alcott nixed them on principle.
Sherlock Holmes/Irene Adler = If Sherlock had ever decided to settle down, it would have been with Irene. Providing he would have been able to get his mitts on her. But then again he was gone a long time after going over Reichenbach falls. ;-)
Henry Crawford/Fanny Price = Well it's obvious from the first that this couldn't happen. I only became interested in it because of the movie. The movie gave Fanny an extreme makeover but it was stylish and I let it slide. But Francis O'Connor (Fanny) and Alessandro Nivola (Henry) had white hot chemistry. It makes me long for Henry to win her over, every time I watch it.
Eliza/Henry - They should have been together. I am just as angry with Shaw as I am with Alcott. But then again, in his epilogue, Shaw states that Eliza spent a large amount of time at Henry's home planning his household affairs. So it isn't as if they completely left each other's company. I'll guess I'll live with the crumbs Shaw threw for this pair.
Those are the pairs I love. But I'm always gathering new ones.