Okay, well this might be a little hard because I don't watch much tv anyway, but I'll try to list as many ships as I can...
Yeah, I know everyone (or at least 99.99999% of fans) think of them as brother and sister only. But I just love the level of comfort these two share. There isn't a lot of tension, arguing, etc. Being scientists, they both understand each other very well and operate on the same (or very similar) wavelength. Plus I think it's adorable when they tease each other and the other light-hearted moments they share. Singularity was the episode that did it for me. Even though Sam is over in Atlantis now (though not for too much longer...) and Daniel was preoccupied with Vala in S10, these two are together in my own silly, delusional little universe. ;)
2. Ships I keep closest to my heart
#1 Jack/Sara (Stargate SG-1)
I know we only saw them together in one episode, but I think they were so sweet together. It's almost a sad pairing, because of the circumstances that they were dealing with. But I think that no matter what happens to both of them, they will still always love each other. *sighs happily*
#2 Cam/Vala (Stargate SG-1)
I just think these two are so fun together. I know most people ship Vala with Daniel but I've enjoyed her interaction with Cam better. I think they have a bit more fun and are a little more light-hearted and relaxed. I enjoyed some of the exchanges they had in Avalon as well as The Powers that Be (esp. the beginning scene in the commissary), and of course Bounty. They've had some very nice serious moments too, like in Dominion. I know Stargate isn't Farscape, but I do enjoy their chemstry nonetheless. :)
3. Ships I love - #1 Teal'c/Vala aka "Tala'c" (Stargate SG-1)
Like Cam/Vala, these two are fun together, albeit in a different way. This scene in Beachhead is one of my favorites between them. "That scene" in Uninvited was also pretty cool (and the one in Line in the Sand) and I just love the playfulness, especially on Vala's part when she calls him "Muscles." Despite the fact I didn't agree with Daniel when he compared Vala to Teal'c in Morpheus, he does share a few basic things with Vala, especially the fact that they're both aliens who've had to get used to the various Earth culture mores and whatnot.
#2 Vala/Tomin (Stargate SG-1)
Like Jack/Sara this one is a bit sad... because you know that Vala and Tomin had a relatively fleeting time together and probably won't see each other again after Ark of Truth. I thought they were sweet together and even though people hate how he treated her sometimes, like leaving her out in the middle of the square for a while and then slapping her in the face in LITS, but I understand why he did it. I wasn't happy with it, but he had this inner conflict going on... wanting to follow the Ori but also loving Vala and wanting her to be with him too. He was such an ardent follower/believer in the Ori that he couldn't handle someone questioning their wisdom. Anyway I think underneath it all we saw how much he cared for her and I think that a part of Vala (at least) will always care for him.
#3 Daniel/Sha're (Stargate movie, Stargate SG-1)
I know, mentioning this one probably contradicts my OTP, but it is one of the canon pairings and I did think Daniel and Sha're were very sweet together not just in the Stargate movie but in the early series as well. Daniel seems to be attracted to women who are smart. And while I think Sha're's smarts weren't so overtly demonstrated (as much as they were with Sam anyway), you could tell in the movie how eager she seemed to want to learn what Daniel was showing her. So, while I'm not as big a shipper of them as I am S/D, I still think they're a very sweet (and again, a bit sad like Jack/Sara and Vala/Tomin) pairing.
"Honorable Mention" ships:
#1 Sam/Sarah (Supernatural)
I don't really ship a lot on Supernatural, but I thought Sam and Sarah were cute together. They had some things in common, like both having lost people they really loved (I liked when she told Sam "when you shut out pain, you shut everything else out too"). I definitely think Sam was attracted to her, but sadly he wouldn't have let himself stay attached to her, especially back in S1 with still being upset over Jess and feeling that everyone around him gets hurt.
#2 Sam/Jess (Supernatural)
I thought they were adorable in the pilot and I liked that Sam was happy with her in WIAWSNB (though at the same time it bothered me that his brotherly relationship w/Dean in that ep was strained, so that kind of spoiled it for me). Her death affected him so much that it was as if he said to hell with trying to live a normal, apple pie life. He just had to track down this demon and kill it.
So I guess I liked the fact that they were happy together.
Um.... so yeah, that's only 2 ships. I can't really come up with any others even though I have assorted ones I like here and there. I don't have much to say about them. I'd add Sam/Dean from Supernatural, but I'm not really a slasher so I don't know if it would count under "ships." I just love the way their relationship as brothers is at the heart of the show. How they look out for each other, are protective of one another, tease each other, the whole nine yards.
Aw what the heck... I'll add a pic anyway :D