You might want to check Alaska Tours and Travel if you want some sort of package (http://www.alaskatravel.com/).

Check into the Toursaver and Northern Lights coupon books for great 2-for-1 offers (their offers come out in October/November). Which book is "best" for you depends on which maximizes your savings. Usually there are flightseeing coupons. Whether you do a glacier landing or a summit flight is more personal preference. I go with the one that has the best coupon offer.

The Whittier glacier cruises and the Seward Kenai Fjords cruises are almost always in the coupon books. Be sure to book a 6 hour or longer cruise from Seward to get the best tour and most wildlife sightings.

The best place to take the train is between Anchorage and Seward. Why? Because it is much easier to get around Seward without a car than around Denali. Also, you could take the train to Whittier and back for the glacier cruise if you wanted.

It is pretty easy booking your own arrangements. Book a car rental NOW though. Even if you won't need it, you can cancel it later. But car rental prices for next summer have been good lately but they won't stay that way.

Stay at least two nights in Denali NP. You need two nights at Denali in order to get deep inside the park. I would book a shuttle bus (not tour bus) to Wonder Lake. If the Mountain is not "out" that day, get off at Eielson and catch a different bus back to the entrance. Be adventurous and get off the bus on the way back to do a little hiking. I just spend 8 days in Denali NP and it was incredible. Shuttle buses, several hikes, 3 days of the "road lottery" (driving your own car into the park) where it took us as long to just get to Eielson Visitor Center as most shuttle buses take for the round trip there and back to the entrance. Incredible wildlife viewing from very close (for example, a grizzly bear 10 feet from our car, looking straight in our faces!).