I have never seen brown spots on headphone cushions that aren't very old. I have no clue what they are. They might be moldy - they don't need to be very dirty to get mold, but if they are in a damp environment it could happen. The pads could also just be faded, or maybe come into contact with some bleach somehow.
I haven't heard the Aiwa noise cancelling headphones at all, but I would tend to believe that the KSC-50s sound better myself, I own a pair of them and they sound incredible for $20. I also doubt they have much deep bass, they might have a boomy midbass (The KSC-50s do too), which can give the impression of deep bass, but while my nice Sennheisers don't have as much obvious thump as the KSC-50s, they play deeper, cleaner, and much tighter.
If you like the noise cancelling part, you need to try a pair of Etymotics. The less expensive ER6s cost $117 and will block out more then twice as much sound as the Aiwas, and the Ety 4 series will block out close to four times as much sound out. Pure music, little to no outside noises.