Season 4 - 8F24 - Kamp Krusty
Fred, Wilma and Pebbles sit in the couch when the Simpsons arrives, in the couch gag to this episode.
Season 4 - 9F10 - Marge vs. the Monorail
Homer: Yabba-dabba-doo !
  Fred: Yabba-dabba-doo !
Simpson! Homer Simpson
He's the greatest guy in history
From the town of Springfield
He's about to hit a chestnut tree

  Flintstones, meet the Flintstones
They're the modern stone-age family
From the town of Bedrock
They're a page right out of history
Let's ride with the family down the street
Through the courtesy of Fred's two feet
When you're with the Flintstones
Have a yabba-dabba-doo time
A dabba-doo time
You'll have a gay old time

This scene is a direct parody on the Flintstones intro. The background music is the same and the lyrics rhymes.
Season 6 - 2F02 - Sideshow Bob Roberts
Bart uses a telephone with a similar receiver to the ones in the Flintstones.
Season 6 - 2F03 - Treehouse Of Horror V
When Homer leaps back and forth in time, the Simpsons' house changes several times.
Season 7 - 3F21 - Homerpalooza

The guy to the left is wearing a t-shirt with The Great Gazoo on it.

Season 8 - 4F20 - Simpsons Spin-off Showcase

Ozmodiar, the alien only Homer can see, is quite similar to The Great Gazoo - the alien only Fred and Barney can see. Ozmodiar has three antennas, in comparison to Gazoo's two.

Troy McClure: So join America's favorite TV family, and a tiny green space alien named Ozmodiar that only Homer can see, on Fox this fall. It'll be out of this world! Right, Ozmodiar?
Ozmodiar: Damn straight, Troy my man!

Season 11 - AABF23 - Beyond Blunderdome
The Flintstones' car is spotted at the museum.
Season 12 - BABF22 - Homr

Ozmodiar pops-up again in season 11.

Bart: Cartoons don't have to make sense.
Ozmodiar: He's right you know!

  Ozmodiar: Oh, you've really done it this time, dum-dum.
Season 13 - CABF19 - Treehouse Of Horror XII
Homer and Marge are dressed up as Fred and Wilma.
Season 16 - GABF07 - Mobile Homer

Bart and Lisa are out driving (!) and checks the map for directions, only to realize that it's a Flintstones Fun Map

Lisa: Hey! This is a Flintstones Fun Map. Look! Dad wrote something: "Dino - short for dinosaur? Remember to ask Jeeves."