It's the shortening of "subliminal tweet" which is directly referring to a particular person without mentioning their name or directly mentioning them and it basically indicates that the tweet in which the hashtag is used is a subliminal tweet.
Basically, it's talking about someone behind their back but sort of in their face on Twitter!
Man, I wish this girl would stop subtweeting about me and just say what she has to say directly. Triflin'!
I wish #oneofmyfollowers would stop #subtweeting and just come out with what he wants to say! Ugh!