Is the CPU position on an AM3 motherboard standardized?

No not all but generally it will be. there are some cases that place the mother board in different heights. especially between the top mounted PSU and a bottom mounted one...then to the Coolermaster Centurion 541 RC-541-SKN1 case mounts the mother board up side down! since home made water coolers usually have the pump/res. out side the case and water blocks inside attached by tubing you cut to length there shouldn't be a problem with space. IF your talking something like the H50 or H70 self contained cooler you need a 120MM exhaust fan opening and they fit most mid/full tower cases. I have an H70 in a COOLER MASTER Centurion 5 CAC-T05-UW case on a 1055T CPU...fit was easy...works fine.