While the first two titles of Doom can be considered the greatest start, Doom 3 and Doom 64 are often considered the black sheep of the franchise. Doom 64 was created by Midway San Diego and was a different look at Doom as a whole.
Rather than just port the same game for the Nintendo 64, to further fill out its capabilities, the game was reformed and redesigned. It had different designs on literally everything, even if the change was more subtle. Rather than focusing on just killing demons, it also has a more developed map system with more advanced puzzles. While the weapons are the same in concept, it even included a new ultimate weapon above that of the BFG 9000, retroactively titled The Unmaker.
It has the gameplay and it has the demon hordes, but what was wrong? The drastic change in graphics put off a lot of Doom fans, first and foremost. Another, even larger problem was that people had no idea this was a totally different game. It was seen as just a port of Doom for the N64 and many overlooked it as such.
It really is a good game, one severe, crippling handicap, though, was the N64 controller. Seriously, people had enough trouble controlling Goldeneye with those weird things. This Doom game had a lot working against it.
Doom 64 was not very well thought of at the time, but since its creation, has grown a fairly large sized fanbase. It was about the same story for Doom 3.
The third entry in the franchise came about after Quake 2, when ID was commonly known and was at the end of their legendary run of games. Doom 3's graphics made so many computers heave and cry due to the sheer weight it put on the system. For its time, it was at the forefront.
The problem was that it was darker, slower and more story driven than Doom ever was. It has many of the demons we know already, adds in a few more and changes up the formula. You're still gunning down hell spawns but you're also finding your way around the under levels of a base in gameplay more akin to Halflife.
For what it was, Doom 3 worked and was fun to play. What put people off was it was not what many called a Doom game. It took a few years to get out of the mentality and allow people to appreciate on its own merits. Today, Doom 3 is highly regarded as a survival horror-esque game that resembles Doom. My real problems with the game involve Spoilers for it, so skip the next paragraph if you don't want that.
(Spoiler Warning!)
Doom 3 is fun to sneak around and fun to shoot with. The real problem is the battle with the Cyberdemon in the game's climax. The Soul Cube was a questionable weapon to begin with and having it be the key element against the final boss was not the greatest move. By then, you've used it so much that killing the boss with it was like rolling off a log.
While these two games are plagued with problems, they are still good. They possess the action Doomers crave and bring something new to the table in terms of gameplay and aesthetics. With how long it took for there to be a Doom 4, these games were good placeholders. Waiting so long for the next big Doom game probably helped us grow more appreciation for these titles. That's a good thing, because waiting over twenty years without them would have been a lot worse. Virtua Hellscape!