The R.Y.N.O. IV. Even in its base form, it is able to kill any enemy in one blast, and its capable of beating Tachyon in less than a minute!
The Gold Groovitron. While its only available in Challenge Mode and costs a staggering 2,000,000 Raritanium, the reward is infinite ammo for the Groovitron. Mind you, the device already turns every enemy and boss in the game into sitting ducks, so removing the one handicap of it—its pathetically low ammo—turns it into a weapon that utterly destroys whatever difficulty the game has.
Let's see. Ratchet ends up in another world, is targeted by the main villain because of what he is, learns about his race and that they were purged, allies with someone who later backstabs him (but in a different game), finds out what happened to his missing father, and after defeating the villain, loses someone who is very close to him. That's quite identical to TRON: Legacy, though Ratchet has more in common with Quorra than with Sam Flynn.
Moral Event Horizon: While all Cragmites are born far beyond this line, it's clear that Tachyon joins his race. But WHEN does he cross it? After finding out his heritage? After his purge on the very species who raised him? After taking over Polaris and ruling it under his Iron Fist? After he brings back his evil race? Or when Ratchet and Clank confront him on Fastoon?
Scrappy Weapon: The Buzz Blades. They're a poor mans Disc Blade Launcher that deal truly abysmal damage, even if you spam the hell out of them, and while its a passable weapon in cramped areas with huge clusters of enemies, its a borderline Joke Weapon when used on individual enemies in open enviroments since due to the lack of walls for the blades to bounce off of. And forget about using them in boss battles—even a suction cup dart would whittle their health down faster.
"Everybody Dance Now" requires you to make all characters in the game dance using the Groovitron. No progress on the Skill Point is tracked, the Groovitron only has three max ammo and its ammo is hard to find, there are lots of similar enemies that count individually, and this also includes bosses and NPCs that appear only once or twice and obscure ones like the six types of penguins created by the Transmorpher and the GrummelNet vendors. You can buy the infinite-ammo Golden Groovitron to help out, but it costs 2 million Raritanium.
"Wrench Ninja 3" on Kortog, but only under certain circumstances. It requires you to get to the Robo-Wings segment while only using the wrench for combat. On a first playthrough its not too bad, but if you skip it and try it on Challenge Mode, it becomes a pain in the ass to get.
"Fast and Fiery-Ous" on Mukow is a frustrating skill point where have to use the charge boots to cross the bridge to the arena without being burned. Not only is it extremely easy to get the timing wrong, if you screw it up, a force field pops up that keeps you from trying again right away.
"Can't Touch This", which requires you to beat the Verigris Black Hole without taking a single hit prior to facing the boss.
That One Boss: Although Tools of Destruction only has three boss battles (excluding the minor ones with the Leviathans and large pirates), all of them will have a lot of HP and will not provide the player with needed ammunition, making these battles almost unwinnable if you run out of ammo.
Tachyon gets a special mention. While he is not too difficult, some of his attacks grant him Mercy Invincibility that can last for several seconds. It gets especially noticeable by using the RYNO on him. Combined with the aforementioned lack of ammo and health and the fight can get rather frustrating.
That One Level: Planet Viceron, aka, Zordoom Prison, especially during the "Escape from Zordoom" mission.