The major file format change that causes the most headaches;
7.0.9 expanded TileData by 4 bytes per entry, changing TileFlags from 32 to 64-bit (uint to ulong)
Also later, when the format changed from mul to uop, it added multicollection.uop and tileart.uop.
These files respectively became the multi.mul and tiledata.mul extensions (not outright replacing them).
The uop file format has not changed since it was first introduced, so all uop files are technically backward compatible with any client that supports the uop format itself. The things you'll miss out on are usually hard-coded features, such as item slots defined for sitting animations (chairs, benches, etc), buff icons (the client retains an internal list of id's associated with their gump id's)... and of course, any clent.exe feature introduced after the version you're using.