Hey, you're right about the Eviscerator, he does look a lot like that pokeman, and even fights a bit like him too!
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Here's another comparison…
Mutant Protopet 
The Purple Monster 
Why?
When I first watched the cutscene of the Mutant Protopet gobbling up Captain Qwark, I thought of the Purple Monster from the Muppet Show (the original show) right away.
They're both big, fluffy, purple and eat up anything that are smaller than them. They even have big black bushy eyebrows too.
To Tipsy: o_0 good lord! that's scary 
To Tipsy: o_0 good lord! that's scary
I don't blame you, that Muppet gave me nightmares when I was 5. 
I don't blame you, That Muppet gave me nightmares when I was 5.
makes me glad I never saw him at the age of 5
You were never a sidekick, you know that right?I always thought YOU were the sidekick
Could be a reference or maybe simply a coincidence but reminds me of how Daxter always thought Jak was the sidekick
AHHH.
That Protopet and Muppet comparison really is creepy 
Nefarious (his pose) reminds me pose from Hulk
Apparently Nefarious makes some famous poses… (Scream )
What's with Nefarious trying to take on poses that already exists? He's not being too original with his shots. 
I don't know if it's only me that thinks of this, but I think Lucy (one of the kids from Ratchet: Deadlocked) reminds me of Pamela from Legend of Zelda, Majora's Mask… but in alien form. It's just the beady eyes, brown hair and maybe even their personalities makes me think of these two quite alike.
Eugene, Vernon and Lucy (this was the only picture I could find of her)
Pamela
If I was able to find another picture of Lucy in her dress outfit, I think the comparison would probably be a lot noticeable.
I just thought this was really interesting… it was posted at the Insomniac forums long ago but I couldnt find it again until now, so… here you go!
(Quoted from Kazumy at Insomniac forum) : Turbo is a foreigner that he finds a job, at the end he had a mision: explorer the galaxy and find the weak point of the Xunguis. Her fiends is Bip, a survivor robot, so the Xunguis destroid his planet.
(apparently, this was made before R&C came out too. And it's a Spanish comic)
But yeah, rather interesting it has a lot of similarities to Ratchet and Clank XD
Holy wow, the main protagonist in the comic does look like Ratchet.
Long ears, yellow fur, pilot suit, uses armed guns as weapons… They look both a like.
The only difference between them is the artistic style and a few small features that each character have and don't have.
I understand that it wasn't originally your comparison Tara, but it was worth showing here. And thanks a bunch! 
EDIT:
I cannot believe I didn't thought of this a lot earlier but do you guys think that Lord Vorselon reminds you of Kang and Kodos from "The Simpsons"?
Lord Vorselon
Kang and Kodos
The difference between the three that one is in a mechanical suit while the other two have tentacles.
I hate to double post here, but I just wanted to bring this thread updated with an interesting character comparison.
When I was watching the movie "the Iron Giant", I thought to myself that the character Iron Giant reminds me a lot like Clank. Even the way they expressed their eyes is almost identical.
Here are the two in blank eye expression.
Iron Giant
Clank
In Sad Expression
Iron Giant
Clank
(couldn't find a really good image of Clank alone with a sad expression.)
Haha this is a very good topic. Has anyone noticed how the Protopets in GC, look just like the Twonkies from the Jimmy Neutron: "Attack of the twonkies" episode? These aren't very good pictures, but it's the only thing I could find.
Those of you who already know what the Twonkies looks like, should see the comparison.
There are few music, what are very similar (for me)
Mid Flute from Spyro Enter Dragonfly by Stewart Copelant
http://www.youtube.com/watch?v=tbJ--Xf9nf4
And Leviathan from Ratchet & Clank 3 (Up Your Arsenal) by David Bergeud
http://www.youtube.com/watch?v=I7HF8CUQZ7A
the "Robo-Wings" track in Tools of Destruction kind of reminds me of the "Troff N Scoff" music in Donkey Kong 64. Both music have the same peaceful cheery beat to it, except the track in TOD has a bit more epic riffs later in the music compared to the track in Donkey Kong 64.
"Robo-Wings" (Ratchet and Clank Future: Tools of Destruction)
http://www.youtube.com/watch?v=FM-ffWT4zA4
"Troff N Scoff" (Donkey Kong 64)
http://www.youtube.com/watch?v=wuorh_PJLsU