... JTAG is that you need to write a bootloader for on-site programming

... serial ISP is that you are stuck if yor thingy does not use serial otherwise, or, for that matter, is not 232

... SPI ISP is that everybody and his brother screw up something and post it as a "working" programming circuit

... all of the above is that too many refuse to pay the nominal charge (SILabs $39, Atmel $25, ...) for the real thing. It is unfortunate that many think they can 'play' with uCs for a $5 investment. This, of course, is aggrevated by the fact that this critical circuit usually is the first thing tackled.

rather than dozens of versions having dozens of slight differences
Richard, I am sure both you and I have finished and released something and then said "I should have done it this way". I guess that, maybe, 'new' silicon technology has something to do with it as well.

Erik