The most basic requirements for qualifying as a "shoto-clone" are a projectile that can cross most of the screen, and some form of rising attack, preferably though not always an uppercut. There is often a third move, usually some form of body-launching manoeuvre that propels the user horizontally across the arena.
The term is derived from the common misapprehension that the martial art practised by Ryu and Ken, the archetypical "shoto-clones" is Shotokan karate. Shoto-clones were very common back when 2D fighting games were at their zenith of popularity in the early to mid-nineties, as many of these games were strongly influenced by Street Fighter, and often emulated many elements of its design. However, shoto-clones are not at all exclusive to games outside the Street Fighter series , common examples would be Sean, Dan, and Sakura.
While a character may qualify as a shoto-clone, and have similar moves to Ryu and Ken, they may function very differently, through subtle qualities of the moves they possess, or due to fundamental differences between the nature of the game that they appear in and the Street Fighter series.
It should also be noted that several characters who started out as shoto-clones went on to shed that status, like a small number of SNK characters.