The Evil Queen Pulsating, Bloated, Festering, Sweaty, Pus-filled, Malformed, Slug-for-a-Butt from the Earthworm Jim video games, cartoon and comics. And to a lesser extent, Professor Monkey-For-A-Head, a scientist with a primate (Monkey Professor-For-A-Head) grafted to his skull.
Then Escape from Monkey Island brings us Admiral Ricardo Luigi Pierre M'Bengu Chang Nehru O'Hara Casaba III. His family has widely dispersed in-laws.
Also, Tales of Monkey Island has Joaquin Jocinto De Meara Alphonso D'Oro, known as just "Joaquin D'Oro". Guybrush is convinced about D'Oro's name that he thinks he should be called "D'Orothe Explorer" (Guybrush's hand slaps him for it).
In Final Fantasy XII, there is just one boss that constantly calls one of the party members, Princess Ashe, by her full name, 'Ashelia B'nargin Dalmasca'. However, it does help contribute to his Hammy moments, so it can be forgiven.
Spell My Name with an "S" and the "L/R problem" gives us the alternative "Andre Laurent Jean Gireux", which is somehow even more French. And you still can't logically get Bebe from it.
King Dedede lengthened his boss fight moniker throughout the Kirby series. Starting with Masked Dedede in Super Star Ultra, became Masked Dedede's Revenge in Triple Deluxe, and Masked Dedede's Revenge DX when fought in the True Arena from the same game.
Salarians have rather long full names. In order, they are the salarian's homeworld, nation, city, district, clan name and given name. A salarian NPC on Noveria introduces himself as Rannadril Ghan Swa Fulsoom Karaten Narr Eadi Bel Anoleis.
While not as extreme as salarian names, quarian names can be rather lengthy; for example, Tali's full name in the second game is "Tali'Zorah vas Neema nar Rayya", meaning "Tali of Clan Zorah, crew of the starship Neema, born on the starship Rayya." At one point in the third game she admits that quarian naming conventions can get confusing even to quarians.
Mika Kuouzumiaiginsusutakeizumonokamimeichoujin from the eroge Resort Boin. That's the longest Japanese surname I've ever seen.
In Harvest Moon, Will's full name is William Terri Luce Andrew Karick Johnathan Toriji Hams Reding Roger Sazak Annick Primus Junior Darshaniack the third.
In Star Control III (yes, yes, it doesn't exist), the Eternal Ones' name consists of their entire DNA sequence, and drives anything that tries to process it to insanity. This includes computers. "Eternal Ones" is taken from the beginning of their name, and translates to every language of every species in existence. Philosophers suspect that Someone's taking the piss.
We get this information, by the way, from the Daktaklakpak. Long in its own way, compared to such species as the VUX or Utwig.
The previous games also had the Ariloulaleelay, from the planet Falayalaralfali.
Jorge Garcia of Backyard Sports's real name is Jorge Raoul Luis Garcia III.
The adventure mode in Carmageddon TDR 2000 has an NPC named "Dick the-most-ridiculously-long-name-in-the-world the Shopkeeper". The adventure mode is activated and played using the game's console, and that every time you need to talk/attack someone, you need to write the command followed by their full name. You can use the up key to re-write a command, but due to a glitch, you'll have to write it all yet again if you do it too many times.
Tumble from Dual Hearts has one, with protagonist Rumble shortening it to Tumble.
Randomly-generated hobo names in Kingdom of Loathing are often this, and can get as ridiculous as: "Burninatin' Gavin "Do You Smell Something Burning?" O'Sullivan, the Guy Who Causes a Temperature-Related Desire to Remove All of One's Clothing." This is appropriate, since the hobos and their names are a reference to the verbosely titled book The Areas of My Expertise.