For me and my family, Ruttles is the eatery we miss most. There aren't any diner type places aside from Perkins which gets old quickly. Ruttles had very tasty burgers, a very nice condiment bar, and some great ice cream treats. We didn't eat there at the end, so I don't know how things were then.
One restaurant I personally miss most is King's Drive-in; located where what used to be called the ISU Credit Union is now. Great onion rings and shakes.
Speaking of ice cream, I also miss the old Dairy King/Cyclone Inn located where Taco Bell is now. At two thirds the cost of Dairy Queen, you got one third more soft serve.
Ah, nostalgia...