El Barto is Bart Simpson's graffiti-tagging alter-ego and is one of the most infamous outlaws in Springfield. El Barto's writings known as graffiti are all around Springfield. This long-running joke has never been unveiled by anyone (except Principal Skinner in one episode and possibly Homer) -law enforcer or otherwise- to anyone in Springfield, even with a large number of clues given throughout the series.
El Barto's signature can be seen in a number of different places around town, especially on state buildings. To this day, El Barto's true identity remains a mystery to the vast majority of the people of Springfield.
However, Bart told Principal Skinner that he was El Barto when Bart and Skinner fell into a vat of Peanut Shrimp. (Although in an episode Skinner said "he's the second worst student, Lisa" right after the mysterious "El Barto." to Lisa.) Homer also seems to know who El Barto is, as he said "If Bart can be El Barto..."
How Homer found out isn't known, but it's possible that Bart told him as well. However, Homer did once say that he suspected that Milhouse was El Barto, even though at the time he was looking at a graffiti tag that showed Bart as Zorro.
Homer tried to adopt a similar alias but gave up quickly because his alias, El Homo, was misinterpreted as saying that Homer was homosexual, rather than the intended meaning of it being a Mexicanized version of Homer's name.
A similar character, El Muerto, was shown tagging a wall. 
El Barto is also mentioned in the Episode "Barthood". Also, in this episode, Nelson finds out Bart is El Barto when they are older.
In "Havana Wild Weekend" Bart is seen tagging the walls of Cuba as "The Bart".
Even though Bart is generally depicted as El Barto, there was at least one instance that implied that El Barto was a separate character from Bart, such as a photograph of El Barto depicting him as an older man who smokes cigarettes.
Note: There's an "El Barto" spray tag outside the Kwik-E-Mart that appears in almost every episode where the Kwik-E-Mart appears. The spray tag also almost always appears at the Springfield Town Hall, on the staircase outside.