I am a fan of the "John Doe" television series, but the "Save As... John Doe" episode is possibly my least favorite of the lot. In the beginning, the guest main character, Paulette, makes her entrance, with German Shepard in tow- inside a bank, that is. Unless it is an assistance dog, canines don't have much place in public areas in general- especially when they lack a leash (which I might add, violates Seattle's strict leash laws). In fact, the dog itself seems like a loose end and pointless beyond a way to track down the stolen goods' location later on, which is in /itself/ ridiculous. Electric collars work by receiving a radio signal from a wire in the ground- they output no actual signal by themselves. If John is able to track something's location by /that/, then a lot of people are wasting their money on expensive GPS tracking systems.
Paulette's supposed boss (AKA virtual lover)'s intelligent house kills the thief of Paulette's case. I still do not understand how it did that (although at least, the image of the man being shocked is far more realistic than the electric-blue mistake in "Doe or Die!"). The subsequent "hacking" involved in this episode is horrible, with messages to off-line computers and John controlling an escalator with a PDA only two examples of many. The scene with John fighting off the two thieves (kung fu-style) and kissing on the gal are equally ridiculous and out of character respectively.
All-in-all, if you have the choice, you can skip this episode. If the series had been continued, perhaps the scene showing the Pheonix Group taking the comatose/frozen bodies away could have become important, but as it stands this is a very throw-away piece of work.