I don't think there is a "standard" way to do ISP (In System Programming). It seems to be proprietary to each manufacturer. I can tell you that Atmel has a couple of application notes on how to do ISP over a modem. Search their web site (www.atmel.com). If your µ-controller has ISP capability you might be able to extrapolate from their application.

I'm just sort of pondering on the fly now, but I wonder if one could write one's own firmware such as to implement the ability to do ISP on one's own. Obviously you couldn't incorporate any new hardware implementations (like a hardware condition to run a bootloader). But if you included the ability to store data to FLASH, it seems one could also develop a few API calls. I guess it would come down to whether you were so married to a particular µ-controller that it would be easier than just implementing one with the feature already built in.