For animals other than the Alaska Highway we found taking the shuttle bus into Wonder Lake in Denali a good route for animals. Bus drivers will stop for photos but you cannot get off the bus for photos unless you are getting off to hike.
We like the Stan Stephens boat trip out of Valdez for marine animals and glaciers as well as the Kenai Fjords trip out of Seward on Resurrection Bay. We have done all of these trips in July and have seen animals on all trips.
For bears you might want to take a trip to Katmai out of Homer in July but this is not a cheap trip. We hope to do this trip this summer ourselves.
Seeing animals along the roadside is hit and miss. We have seen bears on the Alaska Highway and the Yellowhead in Canada and moose in downtown Anchorage and along the Parks Highway.
You can check out the Alaska 2008 blog in my signature to see some of the animals we have encountered in Alaska.