I know it's a harsh world and all, but it seems some of the companions don't really have good endings.

Lily especially has bad ones regardless (she forgets, she stays confused, or becomes a beast)

With lily, the only option I see is the half doses... it's the closest to a good ending for her as anything since she does remember her past and it's left unanswered as to what she finds

a couple of the others seem to be the same way, the good endings are questionable

Not everything is black and white, I'm glad there are gray endings for some things.

Lily needs to move on, so I tell her to up the dose. I wish that Dead Money could have offered some closure opportunities to Veronica with Christine.

Lily's good ending is taking her medicine and becoming sane. It's bittersweet because she forgets her grandchildren, but it's probably for the best that she forgets them; they're part of her past after all. Part of the theme of the game is leaving the past behind, Lily does, and hopefully her future will be happier.

Veronica and Arcade are the real "no happy ending" companions, because they're idealists, and another theme of the game is that idealism never really survives reality. They're not all bad endings, they're just not happy.

To balance it, some of the companions have nothing but good endings, as long as you do their quests. Raul either retires peacefully or becomes a badass vaquero warrior, Rex adapts nicely to his new brain, Ed-E's a robot so it doesn't really mind anything...

Boone has a nice mix, his endings are sad, unpleasant, optimistic, some are also terrifyingly badass. I almost want to get the Legion ending purely so he can spit in the Legate's face.