During Pit's first battle with him, Hades, rapidly punches similarly to fighter/Smash Bros Kirby's Vulcan Jab. He even vocalizes in the same way Knuckle Joe's assist trophy did in Super Smash Bros. Brawl. Hades then proceeds to eat Pit by inhaling him.
Various food items are used as healing items like in the Kirby Series (though they also are used like this in the Smash Bros series).
Super Smash Bros. Brawl is referenced more or less directly in some of the tutorials and a random dialogue when Pit is using a bow:
Palutena: It's a pretty well-balanced weapon. Pit: Yeah, I used one in the last brawl. Palutena: Brawl? How horrible! Were you hurt!? Pit: No, it was a smash! Palutena: I just can't picture you in a melee. Pit: That's because I wasn't...
There are multiple references to other Nintendo games scattered throughout Uprising:
Chapter 5's aesthetic is similar to the original Star Fox 1, the corridor sequences from the Space Armada and Venom in particular. The "outside" sequence erratic background changes take heed from Brawl's Lylat Cruise and Final Destination as well.
At one point of Chapter 20, Pit uses the Lightning Chariot to burst through the shield around Palutena's Temple. It is done similarly to how Kirby takes out the Subspace Cannon towards the end of Super Smash Bros. Brawlís adventure mode. The Palutena Bow, a rare bow unlocked by beating Chapter 24 in 11 minutes or less, is the exact same bow that Pit uses in that game, and scenery very similar to that of Final Destination/Destroyed Isle of the Ancients is seen during the final boss fight with Hades.
When fighting Twinbellows for the second time, Pit says he's going to rack up some serious Nintendogs points.
One of the floors in the Lightning Tower requires you to go up a series of ramps while jumping to avoid obstacles rolling down them. Hades even admits that it's basically Donkey Kong.
When Palutena talks about the powers and how you have to take into account the size and shape of the powers to fit into a grid, Pit proclaims that "All that time playing Dr. Mario has come in handy!"
When you battle the Kraken for the second time, upon knocking it out, Pit will shout, "Take that, tentafool!", a clear reference to Tentacool/Tentacruel.
Computer players in multiplayer have names which many Nintendo fans should recognize, such as "Resetti", "King Hippo", and even "Captain N".
The music to the flying part of Chapter 8 (set in space) bears noticeable stylistic similarity to Mario Galaxy's music.
Several enemies are named after deities and beasts from Greek mythology, though many of these names have been slightly altered (or, more likely, bungled in the translation).
The sound effects of certain shots finding their mark sound very similar to those made by MegaMan Buster shots doing the same.
Thanatos Rising has what's basically a cross between a Trojan Horse and an AT-AT. The Lunar Sanctum level is basically a huge love letter to A New Hope, with Pit assaulting and infiltrating a giant moon-shaped space station with a super laser.
Mimicuties have a rapid-kick move similar to Chun-Li's Lightning Legs. In the final chapter, Hades' fight involves him throwing monoliths at you in a fashion very similarly to the Hadoken motion. And when Medusa shows up to help out, he unleashes a Shoryuken on her.
Some of Pit and Dark Pit's banter between each other throughout Chapter 6 especially the part in the beginning about being a copy can be hard to not remind people of a similar situation and moment between two certain Hedgehogs in another game.
In the game, there's an enemy called "Collin" that can only be killed when you hit back the enemy it fires. The idol for this enemy says the name of the fired enemy is "Phil", and the idol is named "Collin and Phil". Flip the two names around...
Hades's overall characterization and voice seem to resemble Tim Curry, possibly a shout out to the Prince of Darkness from Legend.
The markings on the Ninja Palm are remarkably similar to the ones on Oboro headgear.
A couple of the regular weapons are like this as well.
During the tutorial, Pit asks if Palutena will be sending him a machine-gun toting robot girlfriend, a reference to Curly Brace from Cave Story.
In one of the most surprising Shout-outs, in the Chaos Vortex level Hynden Walch, voice of Viridi, starts slipping in and out of her Princess Bubblegum voice. At first it's rather subtle, with her at one point calling pit a "dingle brain" in Bubblegum's style of speaking. Then later in the level, she says, word for word, and in the same style of the Adventure Time promos, "What time is it?"