Mousefan's theory was that in SKCM, SK stands for "single key". I think this is false.
We know that Alps keyboards have PCBs that come with a code that often reflects the switches used on them. For example, the 12KF086A which comes with SKFL switches, or the 12KC284A which comes with SKCC switches. The actual model codes are even more detailed, for example the KCCAA147 with SKCCs, or the KFFBA010 with SKFF switches. Now note how these don't start with an S, but with a K.
A quick read through the Alps catalog reveals that ALL their switches start with S, not just keyboard ones, but all switches of all kinds. Encoders all start with an E, printers all start with a P. Potentiometers all start with an R, presumably because P was already taken. So, I'm pretty sure S stands for "switch" instead. As Alps keyboards all start with a K, it makes sense the K stands for keyboard. All their keyboard switches that we know of start with SK, while none of their current switches do. In fact, the second letter of the switches on their site clearly indicate what type of switch it is. Therefore, we can assume SK = switch, keyboard.
The CM and CL is a bit more vague, we really only have one hint for this as far as I know, the info sheet on cream and blue Alps:

Now think of the title. Mechanical Contact with Tactile CM Series. Very sadly, we don't have such a shot of linear switches, so it's hard to think of what the L in SKCL could be by anything other than pure guesswork. The title seems to suggest CM is "contact, mechanical", but that would almost suggest SKCLs weren't considered mechanical. So CM and CL are a bit of a guess, but let's keep it at "contact mechanical" and "contact linear" just for the moment. Quite possibly, they're more of an indicator than a direct abbreviation, though.
The addition of the last two letters, like AG and AF, according to an Alps employee who used to make these switches, apparently differentiated the exact type of switches, and indicated operating forces. The colours were used for the employees so that they would not mix up the switches.
Discuss.