Just lightly sand the areas, apply the same sealer and finish as you used originally. It might not be pretty but it will look better and protect the wood from further degradation.

Thanks! Unfortunately we didn't do the original finishing (done by previous owner), so we don't know much about what product was used, except that it was water-based because the neighbor did his floors at the same time with a poly-based finish and wanted to see which "won" over the years. (In theory he wins, but in practice we have an 80-pound dog and toddlers, so...) Would any water-based finish be appropriate to re-seal those areas, given that we do plan to sand it all down in the not-too-distant future, or so I need to worry about creating new problems by mixing the finishes? (Luckily it is a natural finish so hopefully color will not be an issue--although honestly the bare areas are already turning gray/grungy relative to the rest of the golden-toned floor, so I don't think it can be worse!)

There are a few options available to achieve a natural color, but frankly, you're not likely to get a perfect match so I'd pick what's expedient. You could probably start out by lightly sanding the worn areas with 100 to 150 grit paper (with the grain!) and rubbing on a coat of Minwax natural sealer. This should get some of the gray out, bring the color back and protect the wood.
After it dries, you'll need to apply coats of waterborne finish. Call around and find out what brand of finishes would be available locally and I or a local person can recommend a particular product. If there's nothing local, you might have to order something online.

Thank you! Is the Minwax sealer the same as their pre-stain conditioner? (I thought I remembered seeing an actual sealer in their product line in the past, but don't see it listed now.)

Our local hardware store directed me to Minwax Polycrylic as the only sealer they stock that they would try on a floor, but I'm not so sure about that (I've used it in the past for furniture but Minwax advises against it for floors). Otherwise, most of what they carry that's floor-specific are the Bona consumer products--we used the Bona hardwood floor cleaner for a while before realizing it was only for polyurethane-finished floors (which I'm sure did wonders for our water-based finish...) and I presume the same is true of their sealants/finishers/etc. I see that Bona does list some waterborne finishes on their website, so I imagine the store could order these, if one of them would be a good fit (Indoor Wood Oil, Bona Traffic, a few others) but none are stocked.

Another local store recommends Vermont Natural Coatings or AFM Safecoat, though I know nothing about either. We also have a Woodcraft that's a bit of a hike, but is a good source for the harder-to-find products like the General Finishes line, so I can head out there if there's something that might be a good fit there, too.

The Minwax sealer I'm thinking of is the type they carry at Home Depot. You wipe it on and wipe off the excess.
If you can't find anything locally, here's an option:
http://www.amazon.com/s/ref=nb_sb_noss_1?url=search-alias%3Daps&field-keywords=bona+mega&rh=i%3Aaps%2Ck%3Abona+mega
The Bona cleaner is fine for any urethane finished floor whether oil, based, water based or otherwise.