I've just tried to fit a Thermalright Ultima-90 cpu cooler on to a MSi P35 Neo2 motherboard and there is a problem fitting it.

Problem 1: comes from the copper heatsink on the mofets and the mounting bracket the Ultima uses.
The cross bar that hold the cooler onto the mounting bracket is about 1mm or less too long
The Ultima can be fitted pointing up without problems, which would be ok if you have a case with air venting/fan above the cpu (in my case it's a problem)

Solution: Mount the cooler vertically or you need to get out your trusty drimmel and cut away ether
A - a couple of the copper vanes on the heat sink (which might make RMAing the motherboard a problem)
B - Trim the end of the cross bar, This is what I have done it's not as easy to cut the steel as the copper vanes would be but you only need to trim of a little.
There's now just enough room to get a sheet of paper between them.

Problem 2, on the bracket that goes on the back of the motherboard there are two raised sections with plastic feet that rest on the motherboard, you cannot fit this vertically as the wire feet of the solid capasiters are right under the raised section.
Tring to fit it horizontally you get a simular problem with another set of capasiters feet, however they are just at the edge of the raised section.

Solution: Fit it horizontally and carefully trim the edge of the plastic on the rasied section of the back plate, the raised section is clear of the capasiter feet it's just the plastic getting in the way.

Bit of work and the Job's a good'n However if you do not want to go through the hassel of cutting stuff up and cannot mount the cooler vertically don't try this combo.