I'm currently trying to find a 3.0L replacement throttle body to replace my faulty one. I've noticed while skimming ebay that there is more than one part number for that throttle body.

Ive seen 3M4E-CH, 3M4E-CG, 3M4E-CL.
The most odd one is 3M4Z-CH from this page.
2004 Mazda 6 Throttle Body Assembly 3M4Z CH | eBay
I've looked up '3M4Z-CH' on google and returned results for a ford TB.

Does anyone understand the system behind the part numbers?
What do the letters after '3M4' really mean?

 

Ford/Mazda, no diff really. At least for a 15 year or so span. Sometimes a part # will change due to a revision/improvement in the part. Bore size for say at vs mt. Sometimes a part # has been deleted because it was replaced by an updated part. There are many many reasons. Personally i would get the part # from a Mazda online dealer and look for that one because you know it is the best they have. The other #s may be stock Mazda sold in bulk instead of scrapping them.