I'm certainly no pro mechanic, but I can say for sure that creaks and such can be very hard to track down. They often sound like they are coming from places they are not, and even their rhythms are not always a good clue. I had a seatpost once that creaked in rhythm with my pedaling and the movement of my legs, and it took a long time and a lot of experimenting to finally track it down. Anyway, let's address some of your specifics.. In my experience, bearings don't really creak most of the time, they crunch and grind and the noise is usually like a quiet rumble. Though the noise went away when you overhauled the bottom bracket, you took apart a lot of things to access it. Related parts which have squeeked and creaked for me before: chain, chainring bolts, pedals, crank bolts and cranks with a hairline fracture (luckily it didn't break on me before it got replaced). Not saying the overhaul wasn't needed - sounds like it was, but it may not have been the actual culprit, either. If you are really paranoid, you can replace the bottom bracket altogether with a sealed bearing unit for $30-$40, though doing so without the proper tools (and often even with them) can be a real challenge on older bikes.
Sounds like you think the noise came back once, though you question whether it was actually the noise because you haven't heard it since. It can be even more frustrating since it is only intermittent with the rain, but that leads me to think it is likely the chain unless you have recently replaced the drivetrain. No matter how well you keep it lubed and clean, gunk and corrosion builds up over time between the pins and their housings, and will stiffen some links which will be noisy when the chain is dry. That's why it develops after a rainy ride and not during - because the water acts as a lubricant while it washes away your chain lube. Other similar culprits are derailer wheels, which can be very noisy. Unfortunately when a chain is replaced, the rear cogset also needs to be replaced and this can be a little expensive, depending on the replacement. On a freewheel hub, this is an ideal time to repack the bearings since you can only access the cones while the freewheel is removed. If the bottom bracket is any indicator though, it would likely be wise to repack the hubs on both wheels anyway.
Hope some of this helps, good luck!