As scary as some of the other pairings may be, I have seen quite a few that were rather interesting. Here is a list, I'm not sure why, but here goes anyway.
Y
Shuichi X Ryuichi: This is just plain scary to me. Though I do kind of like the pairing, that is, if there were no Yuki. Ryuichi is genki enough on his own, but when Shuichi is added into the mixture, hoo boy, all I can picture is a huge pink mushroom cloud...
Y
Shuichi X Hiro: This pairing does make sense, I mean, after all, they are best friends, and near the beginning of the series, there are hints that Hiro does in fact like Shuichi. All in all, this pairing is totally cute.
Y
Shuichi X Tatsuha: Wow, I guess if you wanted Yuki but couldn't have him, his brother would be the closest thing. I imagine this pairing would be somewhat like Yuki and Shuichi, only the Yuki in this pairing would be a Ryuichi loving, happy looking monk.
Y
Shuichi X Suguru: This pairing doesn't really make sense, though I have read some fanfictions that have made this pairing actually work enough for me to like it.
There are probably a million more pairings out there, if there's one that you like that you don't see listed here, give it to me and I'll put it down.