I started out siding with Caesar most of the way and then switched to the Yes Man quest at the very end, killing Caesar, Lucius, Vulpes at the Fort and then Lanius at the Legate's Camp. Perhaps because I completed most of the Legion quests, for some reason when I first approached Lanius, he was very friendly and asked me to help him kill General Oliver. After realizing there was no way to exit the camp and kill General Oliver, I went back to Lanius and then there was another dialogue that ended with him becoming hostile. After I killed Lanius, the gate opened and I was then able to kill General Oliver and the NCR Rangers.
Other than flying the bomber overhead and dropping 3 or 4 bombs, the Boomers seemed to have absolutely no effect on the Hoover Dam battle. The Great Khans only effect was to send 4 or 5 Khans to the Dam. At the time of the ending, I was Idolized by the Boomers. I completed all the Boomers quests somewhat early and told Yes Man the Boomers would be helping me.
However, later when I was in Caesar's tent it seemed the only way to move the Legion quests forward to unlock Arizona Killer was by telling Caesar that the Boomers would be helping me, which he interpreted to mean that the boomers would be helping the Legion. The update to my quest log seemed to indicate they would suddenly be helping Caesar instead of me. Because so few bombs dropped, I really couldn't tell if they were helping me or Caesar.
Also, I was idolized by the Great Khans at the time of the ending and Papa Khan had told me that I would be his heir. However in the final battle they attacked me. There were so few of them, it really didn't matter, but I expected that they would be helping me.