Against which powers does super senses not work?
Incapacitate, mind control, splash damage, psychic blast, and poison. The rules do not say that it has to be a direct attack against the super senses, but I've heard that there are some powers it doesn't work against. A little clarity would be much appreciated.

Also, If you can't perplex up the damage of someone using RCE, can you perplex up their attack or movement value while they use RCE?

The only power you mentioned that Super Senses does not avoid is Poison. It also does not work against Mastermind. It does not work against those two powers because they are not considered attacks. Basically, if your opponent had to roll two dice to attack your character, Super Senses will work.

If a figure wishes to use CCE/RCE in an attack, then Perplex may not alter any of his stats for that turn---so no.

Super Senses will activate whenever the figure is hit by an attack. If the super power consists of an attack, then it fulfills the criteria. Super Senses cannot activate against Poison, Mastermind or Force Blast for that reason, for instance.

Of the other powers you mentioned---Incapacitate and Mind Control are both attacks and will activate SS. Attacks which are helped by Psychic Blast may also be dodged by Super Senses, as that dodge does not entail damage reduction.