Jewbilee (Season 3, Episode 9)
Moses is represented as a column of light nearly identical to the MCP.
The Tooth Fairy's Tats (Season 4, Episode 1)
"The villain from TRON appears in this episode's opening sequence. (taken from IMDB)" (It should be noted that the character who appears here is, in fact, not the MCP, but rather Moses, who is consistently depicted as the MCP on South Park.)
Quintuplets (Season 4, Episode 4)
"The villain from TRON appears in this episode's opening sequence. (taken from IMDB)"
Super Best Friends (Season 5, Episode 3)
Moses appears again in this episode, depicted as he was in "Jewbilee", as an MCP-like column of light. (It should be noted that the character who appears here is, in fact, not the MCP, but rather Moses, who is consistently depicted as the MCP on South Park.)
Imaginationland: Episode II (Season 11, Episode 11)
Guards at the gates of the castle that Butters tries to enter with the Lollipop king and Snarf are dressed in TRON garb.
Canada on Strike (Season 12, Episode 4)
When the boys are in the waiting room, waiting for their money from the internet, so are a series of internet celebrities, including Dramatic Gopher, Tay Zonday, and TRON Guy.
You Have 0 Friends (Season 14, Episode 4)
When Stan attempts to delete his Facebook account, the computer informs him that it can't let him do that and that Stan will be put on the Game Grid. Stan is digitized and sent into the computer in a scene that is a direct tribute to the scene in TRON where Flynn is digitized. Most of the remainder of the episode is spent inside the TRON-styled Facebook server, with people's "profiles" taking the place of programs and appearing in a variety of colors and some radically varied styles, similar to Data Pushers. Stan is forced to play Yahtzee with someone's profile in a parody of the jai alai game (Stan asks why they aren't doing battle on glowing bikes instead). Stan's profile has taken on a gigantic form similar to appearance to Sark's giant form & the MCP. Stan and his profile do combat, once again, by playing Yahtzee. Stan wins and is freed from the computer.