Please provide the name of your case so that we can make intelligent suggestions... or just take a tape measure and measure the distance between the holes. My guess is that the front and back ones are 120mm and the side is a 92mm. You can go out and buy any fan you want, I'm partial to antec ones, then you can also buy a fan controller with will allow you to control the speeds of all your fans.
Only if your worried about noise. If you aren't super-sensitive to noise, then try and get some fans with a noise level between 30-35db, and you won't need a fan controller. Some people can never find quiet enough fans. GL
You don't really need the fan controllers but I find them useful especially since I have 9 fans (including the one on the psu). You can also get fans that are temperature sensitive and increase rpms when your case is hot and reduce when it's cool.
Yes that's always been the problem with noise. The processor, GPU and chipset fans are usually louder than case fans because they are smaller. You can find some cpu hsf's that have larger fans and so run cooler and quieter.