Last summer we did Anchorage, Seward, Homer, and an Emerald Air day trip to see the bears (amazing!). This year we're going back and using an award ticket on Alaska airlines.
(1) we have a two-year-old along with us
(2) These are the places we can go on that award ticket (BTW we could also fly into one city and out of another)

Adak
Anchorage
Barrow
Bethel
Cordova
Dillingham
Dutch Harbor
Fairbanks
Glacier Bay / Gustavus
Juneau
Ketchikan
King Salmon
Kodiak
Kotzebue
Nome
Petersburg
Prudhoe Bay
Sitka
Wrangell
Yakutat

Any help you could provide would be FANTASTIC! Thank you!

Just about anything on your list. I suggest you do your homework and look at what each area has to offer, and you decide from there, what is the most interest. However, a 2 year old needs to considered very carefully in my opinion.

If you can arrange it with Alaska Airlines, I suggest these two totally different and most interesting cities: Sitka and Nome.

Sitka: Russian past and bald eagles

Nome: Pan for gold on the beach of the Bering Sea

We enjoyed both Juneau and Fairbanks a great deal but I am not sure about a two year old at places like the Museum of the North. I would suggest Glacier Bay. Last year when we were on a day cruise there was a 2 year old on board. He was very good and slept for a large part of the time, allowing his parents to enjoy the fantstic trip. There were also many grandparents that enjoyed the child, it appeared to be a pleasant day for all.

I agree with Castleblanca. Both Sitka and Nome have facilities and accommodations that could handle a 2 yo. Other places like the chain or Kodiak might be a bit more challenging, and the chain especially involves long segments in small planes - not a good time for kids.

Many of those destinations are little dinky towns without a whole lot of tourist infrastructure. Maybe not the best with a two-year-old. My preference would be Juneau and Fairbanks, since you've already been to Anchorage and environs. Scratch Adak, Bethel, and Kotzebue for sure (no offense to any residents - they aren't places most tourists will want to visit). I suppose Dutch might be okay for a day or two, especially if you have an interest in the fishing industry.

My second favorite place in Alaska, after the Kenai Peninsula, is Kodiak Island. It's not nearly as touristy as many of the destination towns in Alaska and the scenery is nothing short of spectacular.

If you have the flexability on your ticket, I'd spend a couple of days on Kodiak then fly to Fairbanks - not because it is such a great destination but because it is reasonably close to Denalai NP.

If you don't have that flexability, I suppose I'd go to Fairbanks and use my time touring Denalai and Talkeetna and save Kodiak for another trip.