I had a client who really needed the possibility of excluding some products from the coupon discount system. After some thinking we came up with a way to exclude whole categories from being discounted. I'll illustrate with a simple example;

Category Coffee is excluded from discounts.
Category Tea is NOT excluded.

We are using a 50% coupon, and the buyers buys;

Coffee Beans @ $50 per pack and Tea Bags @ $50 per pack

So, the shopping cart looks like this (exactly as normal):

I then insert the 50% coupon code, and the view changes to this:

As you can see the coupon has deducted 50% of the allowed item, and nothing from the disallowed item! In addition, you can see that the shopping cart infobox also shows the correct deduction!

Carry on through the checkout:

You can see that the order_totals are correct; $100 (subtotal) LESS $25 (50% of the allowed product) PLUS $5 (shipping) == $80 to pay

And if we now look at the Admin area for the order:

We can see the correct order_totals here too.

This is an extensive overhaul of the coupons system and is in Beta Testing right now.