Foe Yay: Suzu and Tetsunosuke. Come on, Suzu even pretty much comes out and says, after another character asks him why he hates and obsesses over Tetsunosuke so much, that "this isn't hate - this is love."
Also, the ever-smiling, childlike Okita Souji (at least until the swords come out).
Kogoro Katsura, a politician working against the Shogunate, is depicted in the manga as a small man with large eyes who tends to cry a lot. Ryoma even puts a pair of little dog-ears on him to complete the Moe-factor.
The Scrappy: Hotaru for being a wimpy girl who has a crush on Okita as well as being very clumsy. Tetsu and Tatsu for being attention-hogging protagonists despite being cowardly, impulsive and down right argumentative/ disrespectful to everyone including themselves.
The whole series is pretty much compromised of a bunch of pretty samurai crying and confessing to each other their deepest and innermost feelings of sadness. Oh, and killing people.
Well, except that the terrorists they're fighting kill their friends and family, are trying to destroy their capital, and yet actually believe in the same ideals as them. And that Okita's dying of tuberculosis. And that Kondo, Hijikata, Yamanami, and Okita had to assassinate Serizawa because he used his power for racketeering just a year before the series begins. And the fact that, for them, the penalty for any violation of the Shinsengumi rules or Bushido in general, was ritual suicide. So, no, that they manage to be as cheerful as they are is actually quite impressive.