Another classic example of how lack of consistent information (or being too lazy to do research) leads to people making stuff up, especially but not exclusively, kids.
Canonically Applejack is, and always has been, a girl.
I don't really get why people (and this includes writers who, admittedly, might not have been well informed) insist on complicating these kinds of things... It's a simple matter of observation and logic. Most ponies are girls, boys are clearly noted as boys, therefore until proof of the contrary, any given pony is a girl. That's it.
It would be one thing if it only applied to kids' play sessions, fan fiction, said UK literature and whatnot, but when people start putting their personal canon above the real thing indiscriminately when there is evidence as to what the truth is, it becomes bothersome.
Example: I like to imagine stories in an alternate universe where G3 Mistletoe is a guy, married to Stockings and have Merry Treats and Baby Stockings as their kids. But it would be terribly inconsiderate, not to mention confusing, of me to go around referring to Mistletoe as a guy, or spreading doubts about her gender. Granted, this is G3 we're talking about, but still, you get my point.
P.S.: Sorry if I sound harsh, it really isn't my intention.