This thread is rather old but I thought I'd post my solution in the attached zip file...feel free to use it or not.
I've modified the product configuration to allow any individual product to be excluded from Free Shipping by adding an extra radio button in the product's Free Shipping section on the admin page.
I've only tested it on the minimum cart total value. The idea is that if the total value of the cart triggers the Free Shipping module, the module checks to see if there are any items in the cart that should not get Free Shipping.
If the Free Shipping module would otherwise be triggered if those items are removed, (that is, if the total cart value still meets the criteria) the module short-circuits itself and sets a flag that there are Free Shipping items should be exempted from shipping charges buy removing their weights from the order (leaving only the exempted items + tare).
I also made the modifications for total cart weight and total cart items, but didn't test for those conditions. I'd love it if someone would let me know if they do. Heck, I'd love feedback of any sort. I wanted to use Observers to make this work but I didn't have time to research it.
Also, I only modified UPS and USPS. You can follow my example if you use other shipping mods.
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