I can´t see many similarities between Doom´s and Halflife´s storys, except that they both involve a scary kind of alien creatures, although HL lacks the hellish aspect. HL is a typical action movie story, gouvernment has a top secret project in their hidden Black Mesa research labs, then something went wrong...and you are the man, although a scientist assistant, you battle like a one man army through the game, much like in a Schwarzenegger movie.
And Doom? The whole setting is very different, space, military bases and industrial facilities on phobos, something went wrong as well, but they sent you, an elite marine, there to have a look at it...or was it somehow different? Your shuttle crashed and you had to start with the emergency pistol? :)
Ah, and Unreal...it surely had sme very nice moments and some really beautiful designed levels (that Nali water god temple for example), but Zaldron is right, it was just a collection of levels chained together by a weak storyline. The weapons were really inventive, I liked them, and they were not all the same. But the monsters looked stupid, big heads ---> child scheme, not very dangerous...