For me:
Skeletor
Evil-Lyn, Beast Man, Mer-Man
Tri-Klops, Trap-Jaw
Whiplash, Clawful, Webstor
Stinkor, Spikor
everybody else
Evil-Lyn's (most likely) more powerful than Mer-Man or Beast Man, but I'd say Beast man is (arguably) more loyal (I think of him as a bodyguard in addition to general henchman/warrior) and Mer-Man can bring an entire kindgom to the field, so for me those three are on the same level.
I see Tri-Klops and Trap-Jaw as the third "rung" on the ladder, just a small step below the previous three.
The rest are based sort of on "seniority" and sort of on power and sort of on personal preference.
To me, Panthor is sort of outside the loose "chain of command," so to speak. He does what he wants when he wants - he doesn't take orders, but doesn't really give them either.
EDIT: I just read the chess analogy in AmericanLegend's post above, and I think it's pretty accurate actually ...