In short, they were tools, and I used them as such. But that one dog, alone wandering the junkyard in the wasteland struck a chord with me that no other NPC in any Bethesda game ever has. Sure, he was pretty useless. Sure, he had no backstory. But that didnt matter. He was my dog, the Lone Wanderers only friend, my constant companion. I fought to the death for that dog, and woe betide the Raider or Super-Mutant that took potshots at him.
This is why I was overjoyed to hear about animal companions in Skyrim. It gives me, the player, someone to care about.