They're definitely not any kind of worm; as far as I can tell they have egg shaped, ovular, or round bodies.
I looked at some with a bright background and they appear to have several very small limbs on the underside of their bodies, more towards their front; these 'legs' are small in proportion to the body (probably about half as long as the body is wide) and they appear to use them to swim. Also, they are dark brown in color.
On an unrelated note though... when going through some of my gravel I did find a very interesting worm I could only describe as sea-cucumber-like.
I think they do resemble water mites (my initial conclusion 6mo. ago) but I'm just not so sure. Several pages google comes up with says that they pretty much scavenge on whatever is around, but I'm pretty sure mine just eat the algae off my tank glass(plastic, actually); back when I had actual noticeable algae you could see the spots where they had gobbled it up. I suppose this is probably the best guess so far though.
As for substrate, mine is mostly gravel with small amounts of sand and sandy soil mixed here and there. There are many decomposing bodies on the bottom(and I vacuumed Sunday!), but virtually no live buggers. They also don't seem interested in the small amounts of algae growing on my rocks... Just the glass. They spend pretty much all their time either sitting on or scooting around on it... that is... when they're not caught in a current and being blown around.
As far as my Betta bothering any potential future inhabitants, that won't be an issue; he died a couple weeks ago. =/ sure miss 'im.
And finally... I've always liked gobys. I hadn't considered freshwater varieties. Seems like a good suggestion, wikipedia says the biggest problem with smaller freshwater gobies is feeding as they prefer live foods. I may look into that. =)