I have an Aerocool aero-500 which comes with a fan controller that has 3 pin male connector like this one http://imgur.com/DsiPRzy
I accidentally bought 4 pin fans that dont fit in the 3pin male connector. So i cut down the connector and 4pin fans now fit almost perfectly. Picture: http://imgur.com/vSNP3Kh
Is there any danger to it?
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More aboutfitting 4pin female 3pin male
I think you are good, no danger. 4 pin fans are designed for PWM control. That is cycling the fan on and off. But, they work perfectly well in a 3 pin header but at full speed.
A 3 pin fan has a + and a ground pin, usually black and red. There will also be a yellow lead which is a speed sensor. Your fan controller will adjust the speed by adjusting the voltage across the black and red leads.
you are good to go. no danger at all. Welcome to the modding community and congrats on your first experience