Zoomers, Geemers, and their equivalents, especially in the original Metroid. They are impossible to kill on the floor unless you have the wave beam or spend the time trying to bomb them, and they crawl around all those platforms in the vertical rooms, often knocking you off if you mis-time a jump. And they are everywhere.
Metroid Prime 3: Corruption introduced the Phaazoids, an altogether uninteresting enemy with a weak but difficult-to-avoid area attack. It was simple to kill, but was immune to all weapons save the gun that costs health to fire. Many players took to simply running through an area instead of dealing with them, as it often cost more health to kill them than to just soak up their attacks. Adding to the joy was a plot justification for them appearing in every area Samus had 'cleared,' meaning that the further the player is in the game, the more of them she had to deal with. Thankfully, they disappear once their corresponding Red Phazoid is destroyed, which you'll most likely do anyway just for the Gold Credit.
There are multiple enemies in Metroid Prime that can be counted as Goddamned Bats, most notable of which are the Parasites. Only once in the game does a normal, basic Parasite appear individually; in fact, normal Parasites only appear on the Frigate Orpheon, a ship visited in the opening of the game and sent crashing into the planet serving as the setting for the rest of the game. The individual Parasite appears almost solely to give you the logbook entry for Parasites while you still have all the time you need, because the Parasites appear en masse in the "Get Out Fast" sequence after you beat the boss of the Frigate, the Parasite Queen (a giant mutant Parasite created by the Space Pirates), and fling themselves at you and explode in order to inhibit your progress and run out the 3 minutes you have to escape. Another example of Bats, though they are probably less qualified, are the Tallon Crabs which infest the derelict Frigate on the planet's surface. Unlike Parasites, they don't try to hit you, instead scurrying from one hole to the other, ignoring you completely. But there's a lot of them and the less cautious player will walk right into their path to get half a tank of energy blown away.
The scarabs in the Chozo Ruins are basically the planetside version of Parasites that nearly cross over into Demonic Spider territory early in the game, as they can chew up an entire energy tank if you're not careful and blunder into them, at a point where one energy tank is all you've got.
Screw those barb enemies Nightbarbs, too.
Metroids in general. In the 2d games they are difficult enemies that you only encounter near the end. In the Prime series, they're Goddamned Bats. They can be killed rather easily (at least after obtaining Ice Beam or Power Bombs), but attack by latching into your face and blocking your vision, forcing you to go to morphball mode just to get them off. Also, they tend to lurk in dark places and attack from behind, their screech is hell, and there are several times when there are metroids behind a forcefield and you know that sooner or later you have to cut the power and be forced to fight them in the dark. You can at least worry about them less if you have the Thermal Visor...
Fission Metroids in Prime. It's bad enough that that they split in two when you shoot them enough or hit them with bombs three times, and the two parts are only vulnerable to one type of beam, but not the same beam. But when you encounter one, it's during a platforming segment, so when it charges, it'll either knock you off the platform you're standing on, knock you off-course if you were in the middle of a jump, or cause you to panic and risk falling down as you try to bomb it off you. It also respawns after you kill it, and when you get half-way up the room, the game goes "here, have another" and now you have 2-4 Metroids charging at you. And they show up in greater numbers in the Trilogy edition, and in new places too. And in Metroid Prime 3, the buggers can become intangible. Luckily you eventually get the power to kill them in one shot, with a single Power Bomb.
The unique splitting properties of Fission Metroids can be abused, though, with a door. If you walk through a door while a Metroid (including Fission Metroids) is attached to you, the Metroid explodes (for some reason). You can use this to easily restock your health, missiles, and power bombs for the final battle. At the top of the room, enter the next tunnel, then turn around and open the door. Walk forwards until you hear a Fission Metroid screech, then stop. The Metroid will fly to you, so attack it until it splits. When one of the two spawned FMs attaches to you, take one or two steps backwards, entering the tunnel (the door remains open if you're close enough to it). The Metroid explodes, so grab any item it drops. Keep doing this until you're at full.
In both the NES Metroid and the GBA remake Metroid: Zero Mission, Tourian will make you pull your hair out. First, you got the Metroids themselves who are very hard to shake off once they stuck to you. Second, you got the slow moving Rinkas (energy rings) that advance towards you and will most likely get in the way of your shots as you try to freeze and/or missile a Metroid. Third, said Rinkas will likely push you back if they touch you and most likely push you right into a Metroid. Fourth, once you actually get to Mother Brain's room, trying to stand on 1 block platforms as those rinkas and defense turrets (and the turrets can't be destroyed) try to push you into lava as you pump Mother Brain full of missiles will very likely cause you to scream. The remake makes fighting Mother Brain even harder by making it where it's only vulnerable if its eye is open and when it does open, it will shoot an energy wave at you.
Elsewhere in Prime, we have Chozo Ghosts, which have earned a very special place in Chozo Hell for their teleporting tactics, their invisibility to everything but X-ray imaging, their invincibility to everything but the cheesy default beam, their refusal to appear in any number smaller than three, and their visor-screwing, charge-killing lightning attacks. Their nasty habit of dousing the lights and shrieking like demented fangirls doesn't help either.
Space Pirates, if only for their habit of locking all the doors till you kill them all and playing their scary theme music until you do. Unlike the pirates, you can skip fighting Chozo Ghosts when they appear— except if they also lock the doors.
Metroid Prime 2: Echoes has the Darkling Pirate Commandos, spiritual successors to the Chozo Ghosts with the exact same 'invisible warping' motif and a lot more firepower (dark energy beams that mess with your visor and blinding EMP grenades). Fortunately, the Dark Visor is much easier to use than the X-Ray Visor, all weapons hurt them (particularly the Light Beam and the two-shot Entangler/Missile), they only come in packs of two until you get the Dark Visor and they give up and leave if you're still alive after about two or three minutes. An enemy that could have been dangerous made mostly an annoyance.
A very minor enemy, but Metroid Prime's Burrower and its Phendrana counterpart the Ice Burrower were pains in the neck. They spend half their time digging through the dirt, in which case they're invulnerable, then leap up to spit a very fast-moving visor-splattering gobbet of acidic blue slime at you before digging into the ground again. Your window of opportunity to shoot them is very brief, and basically you can only kill them with the Power Beam, as the Plasma Beam doesn't work (at least on the regular Burrower) and the Wave and Ice Beams are too slow firing.
Then there's the Triclops (and their Palette Swap versions in Echoes, the Mechlops). They're immune to pretty much everything except bombs. They will also leave you alone. That is, until you go into Morph Ball form. If you wander too close to one (which is deceptively far away), they'll grab you and chuck you into the nearest lava pit. And of course, they're all over the place in the Morph Ball-only areas of Magmoor Caverns. You have to carefully drop bombs in front of them so that they'll grab the bomb instead of you. At least there's no lava in Echoes.
Another annoyance from Prime 2 that don't know when to quit are Rezbits. They love to move around spastically, block all incoming attacks pretty much the instant you try to make a charged shot, and if you ignore them they'll inevitably knock your suit offline, but you're given which buttons to press to reboot. They also break lock-on constantly if you do try to fight them and are frequently found in areas with tricky platforming. Nobody likes Rezbits.
War Wasps. These little bastards hide in hives that are hard to see if you aren't looking. And just to make sure you are paying attention, they have a very annoying tendency to shoot you in the back with their stingers, which can and will knock you off a cliff if they happen to be positioned correctly.
The puffers and their various incarnations are a regular annoyance. They like to float around, shooting off a noxious gas that can do a lot of damage fairly quickly. Thankfully, you really only run into them in the air, so contact is limited. However, in Metroid Prime 2 Echoes, there are these cyborg puffers called Preeds, which have the same mechanism. You shoot them? They blow up, releasing a rather large payload of kill-gas. Also, by the time the gas has dissipated, a new one has spawns 9 times out of 10. Have fun.
The Metroid Series' actual Goddamned Bats are the Skree (and Shriekbats of the Prime series). They're even worse in Metroid: Other M. Not easy to spot, auto aim does nothing unless they're right in front of Samus, and come down faster than a cannonball off the Empire State Building. But this little bugger is the least of you're problems if you're up against the Desbrachians...
The Flickerbats in the first Metroid Prime are a huge annoyance early in the game. First of all, you can't even kill them until you have the Wave Beam, and even if you do, you must have the X-Ray Visor to lock on to them. This makes killing them a huge pain with the slow-moving Wave Beam (which also has a low rate of fire). To make matters worse, these little buggers just love to fly around erratically and knock you off high ledges.
Hunters has Guardians, which earn a listing here by being annoyingly agile and running around a lot while firing. The more annoying ones are fitted with shock weapons, meaning they fritz out your interface whenever they hit you. Also, they seem to turn up an awful lot during the run back to your ship after you collect the Octolith in a location, and you have to kill them all to unlock the door so you can get away. Occasionally, you will get turned around during the fight (it's easier than it sounds since Alimbic architecture tends towards the proverbial twisty-maze-of-passages-all-alike), meaning you go the wrong way and might have to fight them again.
In many areas in the original Metroid, there are instantly respawning bugs that come out of small tubes, although in Kraid's Lair without the Screw Attack, they can become Demonic Spiders, as they deal around 20 damage without the Varia Suit, and they take two hits. If you decide to go there right after getting bombs, you will die several times.