In Jewel Junction, if the player goes near a gate, they can see a sign that says "WARNING: Private Property", but looking under that text in what appears to be spray paint says "YOU SHALL NOT PASS!".
This is a reference to famous line from The Lord of the Rings.

One of Sunflower's gestures, "Giddy Up", is part of the dance from the music video for Gangnam Style by PSY.

Other plants use the same gesture with a different name, such as Peashooter's "Stomping Peas" gesture.

During the Credits or at the end of Garden Ops, if you look closely at the back window of Crazy Dave's Flying RV, you can see two plush toys of Peashooter and Sunflower, which are official merchandise for the franchise.

One of the hats the Engineer can wear is the 8 Bit Head. This could be a reference to Minecraft, as it's very reminiscent of the game's blocky low-res style.

On the map "Zomboss Estate" it's possible to see the Slenderman in the background of the forest.

The "Garden Warfare" in the game's title is possibly a reference to the Call of Duty: Modern Warfare series.

In the map "Driftwood Shores" in the Gardens & Graveyards mode, there's a boat called the "King of Red Dandelions". This is a reference to the boat called the "King of Red Lions" from The Legend of Zelda: The Wind Waker. An island that looks similar to "Outset Island" from the same game is also visible nearby.

Plants Vs. Zombies: Garden Warfare parodied the Battlefield series in its E3 unveiling, using a similar theme and some of the music used in Battlefield promotional material.