Here's my attempt to break them up. Feel free to reclassify, redivide, or add villains I missed.
S-Level Threats (Call the Justice League):
Darkseid
A-Level (High Threats):
The Joker
Owlman (Earth-3)
Lex Luthor
Prometheus (Grant Morrison)
Ra's al Ghul
B-Level (Major Threats):
Anarky
Bane
Deathstroke
Hush
Owlman (Thomas Wayne, Jr.)
Prometheus (Impostor)
C-Level Threats (Significant Threats):
Black Mask
Blockbuster (Roland Desmond)
Catwoman
Clayface
Harley Quinn
Hugo Strange
Mad Hatter
Mr. Freeze
Poison Ivy
The Riddler
The Scarecrow
Solomon Grundy
Two-Face
D-Level Threats (Send Robin):
Blockbuster (Mark Desmond)
Calendar Man
Catman
Cluemaster
Deadshot
Firefly
Joker's Daughter
KGBeast
Killer Croc
Killer Moth
Lock-Up
Man-Bat
Maxie Zeus
Rag Doll
Ratcatcher
Tweedledum & Tweedledee
Ventriloquist
Mr. Zsasz