Deleted Scenes: There's a number of scenes cut from the movie were included in TV broadcasts (especially in the Hallmark Channel).
Peter washing Chance with a hose after Chance eats the wedding cake.
Kate taking the pets on a car ride. Explaining Chance's eagerness in a later scene when Kate had to leave for the stock drive.
Bob being invited to a barbecue, only for the kids to remind him that the barbecue falls on the day he had promised to take them to visit their pets. Thus the catalyst for the pets' incredible journey.
Kate finding the note she had written Frank that he had not seen, and then calling the pound to know if the pets are found before she realizes they're heading for home. In this scene, Kate realized the pets are going home, and reveals the name of the town the family are from (Fresno).
Sassy observes the man who found her playing the saxophone at night.
The man at the river bringing his goat into his house while he leaves.
Before crossing the tracks, the pets search for food in the dumpster but found nothing, much to Chance's disappointment.
Throw It In: Chance running full throttle into a sapling and then keeping on running (specifically the part where Chance implies that Sassy is fat when rushing off for breakfast) was done completely by accident by the dog actor. They thought it was somewhat hilarious, so they kept it in. Similarly, Michael J. Fox and Sally Field adlibbed the lines right after Chance ran into the tree.
Similarly, Chance stumbling when running through a field was given a humorous line. "Whoa! Gopher hole!"
Homeward Bound II: Lost in San Francisco:
The Other Darrin: Following Don Ameche's passing (the first Homeward Bound was his second-last film role), Shadow was voiced in the sequel by RalphWaite.
Not to mention at least some (if not all) of the animals were recast. Less obvious, but Chance's spots were a different color.