Hey, glad to see that Jnes is still alive and kicking!
I'll be keeping an eye on it more often, now, that's for certain.
As for 98/Me support... I'm debating the same thing in one of my projects. I'll probably end up dropping support for such ancient systems for the same reasons you're debating: 1) They're ancient; 2) Not even Microsoft supports them *at all* anymore; 3) Unicows is "ugh"... IMNSHO, if someone is doing emulation on such an old machine, they're better off using a more stable platform, anyhow. Such as a custom-installed Slackware box, or something.
And, I'm certainly interested in playing with new versions of Jnes. I'm sure some of the lessons learnt from PJ64 will prove to make Jnes one of the premier NES emulators again. (IMO, the title of "best" actively-developed emulator probably goes to Nestopia. But, it looks like you have plans to unseat them!
And, I'm impressed with how happily 0.6 plays in Vista. Just a few minor UI glitches; easy enough to fix, probably. Besides the L10N/I18N effort you're on, adding missing mapper support would be about all I would need to start using Jnes more often again.
Keep up the great work!