Here is a ranking of the most evil Ninjago villains, based on what we have seen in the show, mixed with my opinions.
1. The Overlord
2. Omega
3. Chen
4. Nadakhan
5. Kozu
6. Iron Baron
7. Vex
8. Pythor
9. Reborn Garmadon
10. Skull Sorcerer
11. Samukai
22. Aspheera
13. Cryptor
14. Acronix and Krux
15. Yang
16. Harumi
17. Morro
18. Unagami
The last four villains are those who redeemed themselves in some form, or can be redeemed (For example, Cryptor can be reprogrammed). I also only included main villains (Not sure about Kozu and Cryptor), I didn't include the SoG generals or any evil version of the Ninja (Zane as the Ice Emperor or Lloyd possessed by Morro).
What do you think?