I'm not 100% that the list will remain as it is forever, but I'll give it a shot.
1. The pilot -
It shows how the duo wound up together and how easily Hunter saw McCall as a great partner and not just a beautiful woman who happens to be a cop.
We got to learn a about McCall's soft side, as well has how tough she can be. That lasted throughout the series and I'm glad. We saw that Hunter was determined to treat McCall with respect and not take command of every case.
He wasn't afraid to step across the "line in the dirt" when a suspect drew one.
2. Rape & Revenge -
Lots of soul searching and inner strength came about for both H&M. When each were suffering a personal hell, they were able to step away from themselves for at least a minute to check on each other. Hunter hurt because McCall hurt, and although he was there to support her, he didn't allow his protection to be overwhelming.
3. Unfinished Business -
They were really angry with each other over something more than what happened in the warehouse, but it didn't come out right away. I love that. The tension was strong and it wasn't sexual tension. They wanted to kill each other. LOL! McCall being jealous and hurt for such a long time was finally an issue to deal with and when I found out what they were dealing with I was pretty darned surprised.

I loved the way the scene of Megan Malone at the desk with Hunter (after McCall returns from Quantico) had two totally different spins. Cute!
4. Requiem for Sgt. McCall -
Dee Dee was able to go out on her own and work. I love her determination in getting Steve the justice he deserved. I think this episode (other than Return of White Cloud) really gave McCall a chance to show she can get a job done solo. I thought about Shades, but she had Kitty O'Hearn for help in that one.
I can't settle on one for spot #5, and really should have said top ten. So, in somewhat of a tie, I'll list four other faves without a the reason why. I really need to think more about it, and besides I've been holding out of this topic for too long.
5. City of Passion, The Snow Queen, A long Way from LA., and Return to Justice.