I have a Galaxy S i9000 with CyanogenMod 10 on it which supports both of these commands in adb shell and both take screenshots. They look a little different however.
Using adb shell screenshot:

And using adb shell screencap:

It seems that adb shell screenshot lacks one colour channel, whereas screencap shows all the channels. I tried the same experiment on a Galaxy S4 with 4.4.2 KitKat and only screencap worked, leading me to believe that screencap is a newer version of screenshot.
screenshot worked directly with the framebuffer which is no longer supported in the recent Android versions
screencap is the new version of the tool which works through the SurfaceComposer instead.
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