As far as the naming of files inside the container goes, as Marty said, they can be named whatever you want. I've tentatively decided to name them like so:

If they have an actual ID printed on them, that is what will be used. Just like MESSfan's example:

PAL-MW-0.PRG
NES-MW-0.CHR

If they don't have an ID (like epoxy blobs or eproms) I was planning on either using an implied name (e.g. another ROM with the same hash, that does have an ID) or just use the CRC32 for the filename:

43E95611.PRG
B4C1BFB4.CHR

I'm not sure if I'm going to have support to build images in this format in time for the next release of Nestopia, as there is a bit of behind the scenes stuff I need to get done first. I hope to have it ready ASAP though.

Once nice thing about the database aspect is that Nestopia will still have its huge internal DB with data for carts not yet in my system and then you'll be able to overlay one downloaded from my system on top of his. So your not stuck with one or the other and you can get an up-to-date one at any time without needing a new version of Nestopia to be released.