To be honest, one of the selling point of the franchise always been the ability to make choices and deal with the consequences.
Some of these choices are there to define your character, if you are greedy, altruistic, pacifist, bound to a code of honor.
Many of them include options that are better than others for the people involved. Sometimes, you have to make sacrifices to achieve a greater good.

But there are moment in the franchise you just can't really be sure of what would be the best option for everyone.
Sometimes, you just never end to weight the cons & pros of a decision. Sometimes you are haunted forever by the same question "Did i made the right call ?"

In short, this is the thread about the decisions in which this could be hard or even impossible to be certain you made the right call.
This is also about decisions about things you care about, that make you really scratch your brain about it, even months/years after you played the game. Not unconsequential choices like dying or not in the Jefferson Memorial.

There is no need to select only one.

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Personnally, i recall a handfull of them.

The two main outcomes of Honest Hearts.
I initially thought that the obvious solution was to kick the white legs out, so the sorrows and the dead horses keep their territories.
But if you do this, it weaken the relationship between the two tribes and cause Daniel to lose hope.
If you choose to flee instead of attack the white legs, it strenghten the relationship between the two tribes, and their relationship with the new canaans.
But somehow some characters are haunted by a feeling of regret. Also, the Zion area on itself will remain hostile for a long time.
So, even if i feel that evacuating is a little better, i cannot be certain of it.

About Dog/God in Dead Money, i get that two of the four option allow the shell to live, while not being slave to Dog hunger.
It seems that the fuse allows the being to be complete and in peace, but on the other hand, it feels like God was trapped for so long inside Dog, that i feel unfair to not release him.

There is also the four endings of FoT.
If we had to sum it up, there are two "good" and two "bad" endings.
Amongs the two "good", there is the option to destroy the Calculator and the option to fuse with it.
Contrary to the Fo3 end choices that have next to no consequences, choosing to fuse with or destroy the Calculator produce large consequences in the whole midwest area.
By fusing with the Calculator, you are fusing the BOS army with the robots army, creating a super power that would know no competition.
Choosing to strenghten them so much or not essentially depends on if you support the BOS codex as a whole. Contrary to Lyons crew, this BOS is clearly in the grey area.
Sure, if you are there, you are able to guide them toward the best outcome you think of, but still, you break the balance of the Wasteland.
On the other hand, considering the alternatives in the games, you might think that it is better to drive off those raiders, beastlords and other racists. But creating your own monster make me feel uneasy about it.
(not even mentionning the two other outcomes that could be a disaster for the area)

On same path of these FoT four endings, there are the question of the leadership of Redding (New Reno/NCR/Vault City/Indie) or New Vegas (NCR/Legion/House/Indie) in which all the factions involved have pros & cons.
Also, the flaws of the NCR that FoNV help to highlight turn the choices about them in Fo2, in a different light. I was more inclined to support them initially, for the control of Redding. Now, the decision seems harder than it was.

There are three decision that i would like to highlight, even if i feel they could have been better.

The option of joining the Unity in Fallout 1. Considering it lead to a non-standard ending, it breaks the balance in my opinion.
If you had the opportunity to actually join the unity, become a big green and help to Master to discover new vaults, to go deeper into its teachings, and see actual improvements in societies led by super-mutants (like Broken Hills), it would have made that choice an actual one.
Currently if feel like something you consider in theory, not a choice you scratch your brain about, basically because you don't actually have that choice. (or you have it, but it wasn't given the same amount of content)

I also liked the choices provided at the end of the Pitt. The problem is that the consequences of these choices fall flat.
There is almost no changes in NPC dialogs, there is no slideshows at the end, nothing about short-terms or long-terms consequences.
It really feels like the workd is half done (or quarter done).
On the other hand, it gives a tiny hope in the ability of the Fo3 dev to handle proper RPG.
You have given reasons to care about both groups, enough knowledge of the virus, or the cure to make a call.
And the other hand, regardless the choice you make, you can't make everyone happy, or leave with your hands clean.

The Original Junktown set of ending. It wasn't kept for the release, so it can't actually count.
But basically, the city thrives under the mobster and don't under the honest guy.
It wasn't going beyond that even initially, but i liked the idea of it, and hope it will happen properly in some city in upcoming Fo.