One possible cause for rough/noisy Y axis  

One possible cause for rough/noisy Y axis

I had a problem with noisy Y axis movements, sometimes it would make this sound like the bed slams into something. I found one issue that was responsible for a large part if not all of the problem; maybe this will help someone else who has the similar problem:

If you have Prusa i3 Mk2 and the Y axis movements are rough or noisy, check the Y motor position. When you look down on it, the motor should be parallel to the threaded rods. If it's not - the rear end of the motor is closer to the rods - that's because the Y motor holder has a weakness. The motor is mounted on one edge only (unlike the X motor that is mounted by 3 screws, Y motor only has two). The force exerted by the belt onto the pulley is off-axis and may bend the Y motor holder or even crack it (mine has a hairline crack in the corner below the Y endstop).

The simplest solution to this problem, without taking apart the Y axis, is to add support to the rear end of the Y motor:
http://www.thingiverse.com/thing:2252900
This Y motor spacer clips onto the threaded rods and keeps the Y motor parallel to the rods. To install it, just insert a screwdriver between the motor and the rods and carefully push the motor away from the rods (don't pinch or cut the motor cables, and don't bend the Y holder in the other direction), then slide the spacer along the rods under the motor (not too far, the cable must not get pinched between the motor and the spacer) and let go of the motor, it will hold the spacer in place.