Chibiusa and Jigglypuff (Pokemon)
This is kind of obvious, I think.  For one thing, THE PINKNESS! *twitchtwitch* Must...destroy...pinkness! *cough* Anyway, ehm, Chibiusa and Jigglypuff are both pink (and if you didn't notice that, possibly you should maybe _look_ at your TV next time you watch Sailormoon or Pokemon).  Also, the funky pinecone things on Chibiusa's head look like Jigglypuff ears, don't they?  And they both sing annoyingly and make you want to punt them off the top of the National Cathedral.  Or maybe that's just me that wants to do that.

Ami and Ayanami Rei (Neon Genesis Evangelion)
Personality-wise, they're waaay too different to be clones.  It's just the hair.  Short and blue-ish, although Rei's is infinitely cooler (I looooove her hair and if I had straight hair I would get it cut like that).  Ami's kinda...just...sits there.  In the manga it's cool(er) though.  And they're both quiet, but for different reasons.
 
Nephrite and Tigerseye (both from Sailormoon)
Like Ami and Rei, they're too different in personality to be real clones ('cause Tigerseye looks like he belongs in the Village People and Nephrite, erm, doesn't?).  But their hairstyles are very alike and they're both bishounen villains.
 
Rubeus and Hawkseye (Sailormoon)
Both of their hair kinda looks like flames a little (although Hawkseye...pink flames?).  It's weird 'cause all of the Amazon Trio kinda look like a SM villain from a series past, kinda like Naoko couldn't think up any other character designs for them so she reused her old ones.
 
Zoicite and Fisheye (Sailormoon)
Yup, the Amazon Trio are like other SM villains reincarnated (except they're not, but they look like it).  Zoicite and Fisheye even act alike, crossdressing when they go to Earth and having the same orientation.  The difference being that Fisheye hit on young men (by taking out their Dream Mirrors), but if Zoicite tried anything like that Kunzite would be ticked off.