It's a matter of preference. I don't overclock now, but like the fact that the 90nm consumes less power. Also, I know that if I'm ready to overclock some time in the future I'll have a great chip to start from.
Keep in mind that for the 939 platform, the 3000+ and 3200+ are only available with the Winchester core. The 3500+ is the only socket 939 processor that's available with both cores.
If you want to save a few bucks then get the 130nm Newcastle. If you can afford it, go with the 90nm Winchester.
Newegg prices:
3500+ Newcastle (retail) $267
3500+ Winchester (retail) $290