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The one pixel marquee is great for taking out processing scratches in photo restoration. Let's say you have a photo that came out of processing and there was something on the rollers and there is now a gouge in the photo showing up as a bright line. These are usually perfectly straight since they were mechanically produced in the first place. Take the 1 pixel and make a copy next to the line, then paste it to a new layer and move it 1 pixel into the line. Do this a couple times and the line should be gone. Works for other straight objects too, but the object has to be perfectly straight for it to work.

I also would use it for creating interface patterns and such as BigCloud points out. (although for scanlines or pin-stripes, I would probably just make a pattern).

More than anything, I think it had a couple uses (more back in the day before layers and such) and it's still there for completness. It does have a couple uses, but no, to answer your question (sorta) you aren't missing out on anything major, it's just there.