After everything I've been through in the Mojave, I've come to realize that everyone - NCR, Legion, and House - are all to incompetent to be able to run New Vegas to the largest amount of the population. I've never picked the Yes Man ending, because I can't find a way to justify anarchy. Are there any choices I can make with Yes Man that can ensure a good ending for the majority of the Mojave?
With Yes Man himself? No. He only lives to do as you tell him to, up until arguably after the end of the game (I won't spoil it for you).
The best you can do is work with the individuals and groups all over the Mojave to make sure that each of them can live the best they can on their own:
Complete the game with good karma - it will dictate The Courier's general behavior after New Vegas is independent.
Take care of things with Tabitha on Black Mountain
Give Raul some direction (complete his quest)
Become idolized by the Boomers and fix their plane
Ensure Elder McNamara remains head of the BoS, and have them sign a treaty with the NCR
Kill the entire Fiend leadership
Ask the Followers of the Apocalypse for their support
Meet Arcade's friends and ask them to support the NCR
Kill the Powder Gangers in Goodsprings
Help Cass out by gaining evidence of those that have wronged her
Convince Papa Khan to just leave the Legion and to build a legacy for the Khans
Help the doctor with his experiments in Jacobstown
Convince Lillie to take the full dose of her medication
Broker a peace between the Kings and the NCR
Find Rex a new brain
Get the Misfits to cooperate with each other at Camp Golf
Help the Bright Followers west of Novac GO TO SPACE!
Help Boone let go of the past
Blow away the Powder Gangers at the correctional facility
Convince the Powder Gangers at Vault 19 to surrender
Get Primm a new Sheriff
Get ED-E upgraded by the Followers of the Apocalypse
Let Chief Hanlon at Camp Golf continue to do his thing at Camp Golf for the Rangers
Note that some of the choices above are my subjective opinion on the "best" ending for them, in terms of what's good in the most altruistic sense for the citizens of the Mojave should you try to win their independence for them.