You can do this with
Total-Based Shipping. You'd use a 0.00 shipping cost for free shipping, and then a rule like this on the charge so it ignores products on Special:
Rule: Total Value = Non-Discounted Sub-Total
For example:
------------------------------------------------------------------------------
CHARGE #1
Title: Free Shipping Over $100 (not including products on special)
Sort Order: 1
Charge Field: 100-99999 = 0.00
Rule: Total Value = Non-Discounted Sub-Total
------------------------------------------------------------------------------
Feel free to take a look at the screenshots and demo site, and if you're interested let me know at
www.getclearthinking.com/contact if you have any further questions.