I can give you a list of texture parts that can be transparent for you. It's incomplete, but this is what I know so far.
1: Eye iris and Final Smash eye textures can be transparent if they're not flat-eyed.
2: Link's sword.
3: Portions of Samus's legs.
4: The visor on Fox's/Falco's headgear.
5: Peach's/Zelda's dress.
6: Almost all of Ganondorf can be transparent. Only his hands and eye base can't be transparent.
7: Pit's wings.
8: Zero Suit Samus's ponytail.
9: Ike's cape.
10: Most +2 textures can have transparency, but only for certain areas.
Most of Sonic's head and body can be made transparent.
Though its not very useful.