In Episode 7, after reading Bowser's letter, Mario says (in relation to Bowser's mention of eating a goomba), "Imagine being in Bowser's digestive system!" Coincidentally, one and a half years after this episode was released (which was 2008), the game Mario & Luigi: Bowser's Inside Story was released (in 2009), in which the brothers spend most of the game traversing Bowser's body.
The show's characters are primarily based on Super Smash Bros. and other Nintendo series. However, Capcom character Ryu ended up joining the show several years before he was announced for Super Smash Bros..
One of the major plot points from Episode60 was that the Darkness had survived his death at the hands of Wario by effectively turning his hat into a Soul Jar and then getting rid of it; he later transferred himself into Ness's head when Ness put on the hat in the "Operation Blind Storm" special. Flash forward to 2017, and we get a game in which Mario can effectively do the exact same thing!
Ash and Brock (and when Ash left, it became Brock and Gary)
Hype Backlash: Season 5 to an extent. It left Richard really upset as he believed he had wrote the best season ever for the finale and having read the negative reviews really bought him down. It thankfully died down with episode 75 which fixed up most of the season's problems and delivered a truly great ending.
I Knew It!: Wario being the second Chosen One was one of the main theories of the fans
Narm: The blood effects used in one of the later season 3 episodes may come off as a childishly gratuitous attempt at Darker and Edgier. The creators may have realized this, because for some reason future fight scenes lack this effect.
Then in the finale, it is revealed Mario was significantly weaker during that fight.