CJ2001 - In n Out burgers are one of those places that a lot of the Aussies here like to go to. Its been a long time since I've eaten at In n Out because there are so many other good burger places in the US and I like trying something different. I haven't been to the one at Fisherman's Wharf so I'm not familiar with how it is situated inside.
There is a Rainforest Cafe at Fisherman's Wharf; which is on Jefferson. If you've never been to RC, it might be worth trying out.
I've eaten at Lori's Diner which is at Ghiradelli's Square. The decor is very Americana and pure diner. The food is variable; but if you stick with the burgers, fries and milkshakes you'll be fine there. It's on the upper level and the view isn't too bad.
Both RC and Lori's should be fine for kids; although it can be noisy at Rainforest Cafe.
However, if your kids love eating fish and chips, and you're at Pier 39, check out either Neptune's Seafood or the Pier Market Seafood. The views from Neptune are spectacular! If you can score a window seat at the Pier Market, you'll be treated to views of the Sea Lions and the bridge. From memory, both the Pier Market and Neptune's offer a kids menu and colouring in papers and crayons (like most restaurants in the US).