You are in for such a treat in going to Alaska. We have cruised in early July and late August and I can't imagine that September will be a lot different than late August. As everyone has probably mentioned, the White Pass Railway in Skagway should not be missed. If you're looking for an economical way to spend sometime in Juneau, you can take a bus to the Mendenhall glaciar for about $5.00 each way (just outside the cruise terminal) and spend a lot of time inside (seeing a movie for a few bucks more) and hiking trail - absolutely free -- we saw a mother bear feeding her twin cubs salmon from the river right in the park last August.
We found Ketchikan to be the best for souvenirs as far as selection and prices. Since it was our first port, we didn't take advantage the first time, but certainly did the second time.
If you're in Vancouver before your cruise, I'd also recommend the Whistler Mountaineer that takes you up to the Whistler Mountain where some events for the 2010 Olympics will take place. You can spend the night or return the same day.
You're in for a real treat -- lucky you.