What is the difference between disk brake rotors? Differences in rotors include size, thickness, pattern cut out of the metal and attachment to the hub. What other differences are their and why? Reason I ask is I recently built up a budget mountain bike and most parts I bought or borrowed from other bikes. One part I borrowed is the discs from another very cheap mountain bike I had (an Apollo) - they seem thicker and heavier than the discs on a Kona Hoss that I have. The brakes on my bike build aren't working brilliantly. Braking is ok but there isn't much modulation. They aren't expensive brakes but they were bought new - Shimano alivio and I'm wondering if the type of discs do play a part?

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There's also the rotor design.   There should be holes such that the whole brake pad presses over a void, and several times in the rotation.  Some really poor rotors don't have holes arranged right, so one circle of rotor is plain metal the whole way.  This doesn't clean the pad and contributes to bad braking.   

Thickness is partially to cope with heat.  More mass takes longer to heat to extreme levels.  Less mass is lighter for riding.  Also thicker rotors will resist bending more-so than thinner ones of any quality.

Rotor Size or Diameter is a design thing, not a quality thing.  You need the rotor to suit the location of your calipers, and they will depend on the fork mounts and the rating of the fork.  Same goes for the ISO 6 bolt holes or for the centerlock style - it is yet another competing standard with relatively minimal effective braking differences.