Don't mix the throws with the controls... technically know matter what you do... nikkyo is never a throw as such... it is katame-waza or osae-waza (controlling or pinning techniques) and nage-waza (throws, plain and simple)
Anything can be very painful when crossin the line between the true Aikido and executing Aikido techniques
My worst moments have been koshinage (trying to get up and start breathing normally
And surprise-surprise - Techin-nage after my sensei discovered that it's cool to hit you down with practically a very strong shomen and call that also a tenchin-nage. Shihonage is everyday pain
Of controls... uhm... nikkyo would be my pick... especially some freaky derived variantions.
Aikido techniques can be very painful, injuring and deadly... true Aikido in whole - NEVER!