So, I found the TPS61099x series of boost converters, which claim 1uA quiescent current and 75% efficiency at 10uA load. These look usable out-of-the-box for micropower 1-cell MCU applications. I do wonder, though, if the same shutdown trick can be used to reduce the sleep current even more by running the converter at higher current (and higher efficiency) to periodically charge some low-leakage storage caps. I'm going to order a few and test them out.
The downside I can see to this part is that the only package option stocked at DigiKey is a 1.23 x 0.88 mm BGA. That's pretty small to assemble at home.
Another small PCB from OSH Park coming up. At least I'm batching them now, so they don't have to send me an envelope for $1 worth of boards :-)