I’ve heard (friend of a friend stuff mainly) that some people don’t realise their local McDonald’s/Burger King etc. are part of a chain. This seems far fetched but not impossible. A friend of mine was raving about this cool restaurant in Dublin, this unique, funky little place called Wagamama. It turns out to be a chain of 50 or more restaurants throughout the UK and Ireland. Have you ever eaten in a chain restaurant and not known it was so?
We ate at a PF Chang’s without realizing it was a chain. The food was good but not great.
The first time I ate at Popeye’s I thought it was unique. I even asked the counter drone to compliment the chef. He looked at me funny.
Damn, I miss that place!
There’s a sandwich/wrap shop nearby called Camille’s Sidewalk Cafe. I thought it was local (because it seemed local), but apparently they have locations in 27 states.
There is a French restaurant called la Madeleine that I thought was just a cute place here in Washington DC. Then I went to New Orleans and saw one! Really pretty good though.
Macado’s (smallish and regional, but still a chain). Had no idea until I heard someone talk about going to one in Boone.
I had never heard of Red Robin the first time I ate there, but it had a chain vibe, so I figured it probably wasn’t local. As a kid, I never knew that the Ground Round was a chain - it was so cool and funky, with the peanut shells on the floor!
Joe
I didn’t actually eat there, but I didn’t realize Morton’s The Steakhouse was a chain until this weekend when we went down to Anaheim and found another one. I thought it was a local (SF Bay Area) restaurant. Now, looking at their website, I see that they’re all over the country.
Wan Dzu Ji makes excellent Chinese food, including several varieties of Szechuan noodles and tofu dishes that are spicy enough to give you nightmares. The restaurant in my old neighborhood looks rickety and unpolished enough that I thought it was a single, locally-owned shop. Turns out there are shops all over Tokyo (and perhaps all over Japan).
I once had a friend who prided himself on being very knowing and sophisticated, so when I visited him in San Francisco, he wanted to take me to a fantastic new restaurant he discovered in his neighborhood. I would love it!
So where did we go? Pasta Pomodoro! Don’t get me wrong, I like PP a lot, but you had to see his face when I told him that his “discovery” had a dozen chains littered around the Bay Area, including one two blocks from where I lived in Oakland. 
We ate at Cafe Tu Tu Tango while in Florida; not only did it turn out to be a chain, there was one within 20 minutes of where we were living in southern California.
The first time I ate at Romano’s Macaroni Grill I didn’t know it was chain. Admittedly I hadn’t really thought about it much but I remember seeing another one later on and realizing it was part of a chain.
I’ve had the opposite experience. There’s a restaurant I like in Houston called Wraps International Burritos. I eat there a lot because it’s near my sister’s house. I always assumed it was part of a chain because it seemed like a chain-type place. But one time I did an online search to find their other locations in the city and I found that they are in fact just one restaurant.
For a long time I didn’t know Le Peep was a chain. I thought it was a stand alone in Steamboat.
The 94th Aero Squadron in San Diego. I thought it was a charming little WWII themed place. The dicovery that it was a chain made it less charming…
I always thought Steak & Ale was a unique place; the only one I ever saw was near Crabtree Valley Mall.
When my daughter and I were in Long Beach, we first ate at Mimi’s . I didn’t realize it was a chain until I saw one in Anaheim and then, we got one in Reno. Pretty good food.
Pizzeria Uno (now called Uno Chicago, I think). Thought it was a local pizza joint for quite a while. It was a lot better than a Domino’s/Pizza Hut type place, but I haven’t been there in a while, so maybe has changed.
Ate at a Bucco di Beppo’s in Palatine, IL. Enjoyed it, and had no clue that it was a chain – there are none where I live. I thought the kitsch and Frank Sinatra shrine were authentic.
About nine years ago, a friend from Florida was ranting and raving about a new restaurant that recently opened there, and crowed about how there was nothing like that in my home town of Boston.
The restaurant was Boston Market.
While living in New York, I went for some Sybase training in Dallas. We, the students and instructor, decided to have dinner as a group rather than eat seperately. Never realized **Macaroni Grill **was a chain til I moved to Colorado and found several here.