Heh, don't know how I went so long without hearing these pointed out!
I know there's a lot in ZUN's stuff, the only one I recognized was a Neon Genesis Evangelion reference (though others have claimed it comes from elsewhere):
To be honest I think it's pretty unfair to call any of these examples plagiarism - a lot of these riffs are fairly accessible and not exclusive to the tracks mentioned.
Ghignarda, please tell me where anybody claimed somebody has plagiarized anything. All I ever did was to say that Kondo got heavily influenced. I never discounted his works.