MSI Afterburner is used the most because it works on any card regardless of brand. Software like ASUS Smartdoctor, Sapphire's Trixx and I assume EVGA's precision only work on their brand of cards. As a result, MSI gets a lot more attention and use.
I can tell you that ASUS smartdoctor has many problems, so I definitely wouldn't use that, but I do not know how good EVGA's precision is.
Like bystander said, MSI Afterburner works on any brand of Graphics Card (PNY, EVGA, MSI, etc). IF you have a MSI graphics card then you can adjust the Voltages of your GPU with Afterburner; if you don't then you just gotta work with what you can.
I, myself use Afterburner and it's great! Very easy, very user-friendly. You can easily adjust the speeds in real-time, and I've never had a problem. You can also allow it to apply overclocks as start-up automatically, which is a nice feature. The way you can adjust the fan speed based on the temperature is a great feature too.
I've never used EVGA Precision so I can't really compare them both. But you can easily just write down the overclocked speeds you have right now, and just put them right into Afterburner with no problems. Literally it's as easy as 1, 2, 3.
Actually, MSI Afterburner does let you adjust voltages on non MSI cards, but not all non MSI cards (usually newer models). At least it works on my XFX 6950 the same way it works on my MSI 6950 TF2 (though it could be made more consistent.)