Yeah this has always been an issue for me as well. I said screw it and went to industrial fans on everything and haven't had one problem since. Technically the 25mm fans are the "right" size, but if you clock the 30mm a degree or two, they still allow you to screw to the heatsinks.
I was using these 5V "FAN VAN" fans for a while...
5-6V Fans 1"
However I have since gone to 12V high output fans like these:
The 12V fans can get a little thicker 10mm - 15mm - 20mm, but mounting space has never been a problem. In this post you can see the thicker fan I used to keep the Tekin R1 cool. The thicker the fan box the more efficient it is and the more air it will move. The other cool thing is that you can plug a 12V fan right into a 4S pack without any problems and it will really keep things cool. I have been doing this for about a year now and have never had an issue. These 12V fans move loads more air than the crappy RC fans we usually have available to us and as you can see these are MUCH beefier.