Well ordering is pretty easy. Pikmin always go in the same order when you blow the whistle. That is Red > Yellow > Blue > White > Purple.
As far as damage is concerned, i dunno about all of the attacks. However knockback varies depending on which Pikmin does the ATK.
Example of killing moves:
Fair/Dair/Bair: Red pikmin have most, then Purple > blue > yellow > white
Any smash: Purple > red/blue > yellow > white
bthrow/fthrow: ALWAYS blue
uthrow: purple
A good way to get a kill is land cancelled nair an opponent (ie. land before nair finishes so there is no knockback)... then usmash etc.... virtually inescapable.
Pseudo combos:
Almost always started with dthrow. Best if done with a yellow, so there is more hitstun. Eg... (my fave) dthrow > fair > fastfall > regrab > dthrow > usmash > uair.... or forget about the 1st half and throw and smassh since fair > regrab doesnt always work.
dtilt can also set up at low % to a usmash
pikmin toss is very very good. use it!!!! think thats the most important stuff... anything else?