Basicly there are 3 different versions of Capitole: the original Capitole (now known as mk I) ca. year 2000, the most popular mk II (2002 me thinks) and the latest Reference (for whatever reason instead of going for mk III sufix they named the new player Reference).
Mk II and Reference models can be had with the SE modification, which replaces the original Hovlands caps with vastly superior V-Caps. This mod was first offered by Globe Marketing - AA distributor in the US - but now a player can be ordered with this mod from the factory. To add to the confusion, this mod is called by AA "Signature" not SE, although it is exactly the same.
All the models have tubed output stages and superior Philips CD-Pro2 drive (not shure about the mk I though).
The model representing the best value (IMO) is Capitole mk II SE, which can be had for around 5000$ used. I was told that it is actually superior to the plain vanilla Capitole Reference (without the SE mod).
Hope it makes sense.