Joe Simon (1940-1941): Co-Creator of Captain America, and one of Marvel's earliest resident talents.
Stan Lee (1941-1942, 1945-1972): Certainly the most famous in comics, and even those who think Jack Kirby and Steve Ditko did most of the hard work will acknowledge Lee as the most important editorial hand in the history of comics.
Vincent Fargo (1942-1945): Handled the company while Lee was doing service in WWII. His main impact was a large amount of Funny Animal titles.
Roy Thomas (1972-1974): A natural choice to follow in Lee's footsteps, as the first Promoted Fanboy at the company, and was the writer with the largest pull after Lee.
Len Wein (1974-1975): Was editor for the briefest of the times, but he did make his mark by reviving a little book called X-Men...
Marv Wolfman (1975-1976)
Gerry Conway (1976)
Archie Goodwin (1976-1978): Would later make his mark handling Marvel's epic line.
Jim Shooter (1978-1987): One of the longest lasting and most controversial editors. Helped electrify the company after sagging sales, and spearheaded many beloved runs, but his tenure came to an end amidst micro-managing the talent, and conflicts with the powers that be.
Tom Defalco (1987-1994): Succeeded Shooter, and was on board during the comics boom of the late eighties and early nineties. Interestingly, despite presiding over a period that was considered speculation-heavy and crass, he managed to deflect a lot of ire the industry pumps like oil. This is probably largely due to his laid-back persona, his quietly going back to writing (including the fan-favorite Spider-Girl) and Ron Perelman nicely positioning himself as the Big Bad of the era.
In 1995, the decision was made to split the editor-in-chief position five ways. This lasted only a year, as Marvel's line shrank drastically.
Bob Harras (1996-2000): Gained prominence by more or less running the X-Men line, so that when the editor-in-chief position was consolidated again, he was pegged as the natural choice. Word is, Harras made his enemies around the office, and some were not pleased at his resolution of the The Clone Saga (though to be fair, it was an inherited mess), but what may have ended his tenure was the inability of the X-Men comics to resemble, let alone capitalize on the upcoming film. Although a great deal of titles were bland, directionless, or even experiencing a Dork Age through his stewardship, a few of his efforts were positive as well. The majority of the non-mutant characters were reinvigorated and finally given top-notch creative talents in the aftermath of the Heroes Return event which was sadly at the expense of the X-Men. Deadpool was tested out with his own book, and has become the Breakout Character of the nineties. Harras also greenlit the Thunderbolts, a property that still sticks around here and there.
Joe Quesada (2000-2011): Currently Chief Creative Officer of Marvel Entertainment (which includes not only comic publishing, but video games, films, etc.), and the second longest-serving EIC of Marvel Comics. Started out as controversial, but got some good notice for cleaning house at the company. However, is now controversial for storylines like "One More Day".
Axel Alonso (2011-present): Current editor-in-chief of Marvel Comics. Alonso's appointment was well-received by Quesada's critics, but it was quickly clarified that Quesada was being promoted to Chief Creative Officer of Marvel Enterprises, not fired. Thus far, Alonso seems infamous for his distinct lack of infamy compared to his predecessors.