Labeling them incrementally doesn't actually help. Imagine the following situation:
We've got the original Pyra, version 1, with the basic board and the OMAP5 processor.
Next is the UMTS enabled Pyra, version 2, with the cell module and the same OMAP5 processor.
A year passes and ED releases an x86 module. With basic board we'll call that 3 and with cell module we'll call that 4.
At this point an application can say "works on version 1 and 2, but not 3 or 4". Could be better, but not too complicated.
6 months later he releases an A80 module: we'll call this 5 and 6 respectively.
Now we have an application that might say "works on 1, 2, 5, and 6 but not 3 or 4". We're getting more complicated.
Now ED discovers a bug in the x86 board. Nothing major, but still something to be fixed. Version 7 and 8, to add to the confusion.
And then he releases the 4G board, and we have versions 9 through 16 which are all software compatible with their basic and 3G counterparts.
And the numbers themselves don't tell you anything about what you've actually got inside the case. Is version 87 in some ways better than version 62? Or are they different branches?
There's merit in Binky's proposal, it's useful to separate features. If I've got 1.2.3.A, and notice there's a 1.2.3.B version listed, that might mean there is a new version of the CPU board I want to look into. If I've got the 1.2.3.A and there's a 1.2.4.B, that might mean an entirely different board got an upgrade and I don't care about that. Users can write software which pings these versions and they can know "I'm running on the OMAP5" or "I have a 3G or better module" just by looking at these codes.
Of course, as they come out they'll probably get sub-names as well. An x86 module might get labeled Pyra-X and the 4G board could be "Pyra-4G" (so the x86 on a 4G board might be "Pyra-4GX"?) or whatever. No point in fussing about these if they never come up.
But sane versioning numbers doesn't hurt to have, and at the least we know there'll be three version: basic, 3G, and 4G, which are all basically compatible but applications might like to know the difference anyway.