* Judy's quests ending
* Panam's quest ending
* Maelstrom quests ending
* Sinnerman's quests ending
* The fact you can end any assassination quest with killing the target or kidnapping them
* Us Crack/Kerry's ending
* Kill or Spare the Voodoo Boys/Side with Netwatch
* Save or let Goro die.
* The four endings of the game
No, the random monster attack equivalents don't have multiple endings but you have huge numbers of choice sin the game.
Save Brick and he'll help you later in the game.
I'll have to agree with Mebrilia here.
It's not that the game doesn't give you choices. It's the outcomes of said choices that's highly disappointing and ultimately meaningless. So much so that in reality it's mostly the illusion of choice that's presented to you.
Let's take the Voodoo boys as an example. You can either cut off the heads of the gang or let them live. But does it really matter? What effect does it have? What meaningful change is there?
Let's look at Maelstrom's quest. No matter who you side with and which Militech suit survives, they'll both just hand you a piece of highly classified and experimental tech. No matter what your previous choices were. Sure, Brick will help you if you helped him but it's also irrelevant because if you sided with Royce, Royce appears in his stead leading to the exact same result.
Let's look at saving Evelyn. The cloud 9 conversations offer you a ton of choices. One of which is with the first doll. Once you wake the doll up, you get 3 choices. Threaten, bribe or ask for info. All three end up exactly the same - the doll gives you the information you want. Talk to Woodsman, whatever you say, you'll get the information. If you did Shabo's quest beforehand you can use it to accelerate the conversation but it all ends the same way.
The list goes on of completely meaningless choices. The only one I've seen that I felt was actually meaningful was Claire's quest. It's highly disappointing to have so few meaningful choices in a game that looks like it's constantly throwing choices at you. I haven't even seen them all because I'm trying to make this last as long as possible but to say the choices have an actual impact on the game is, in my opinion, wrong.
If, depending on which suit survives, you acquired the flathead even slightly differently it would make a world of difference.
If not saving Brick meant you didn't get help and it made the quest harder, it would make a world of difference.
If the doll in cloud 9 told you to shove it when you threaten her, or gave you less info when simply asked politely or some variation that would have you find the information you need differently. It would make a world of difference.
If the new leadership of the Voodoo boys decided to put a hit on you and you get some quest to fight them or some random event where you get attacked. It would make a world of difference.
I could keep going but I don't really want to. The consequences do not have to be world altering to be meaningful, but this lack of meaningful consequences is definitely disappointing to many.