Here are my picks for the top five most iconic covers featuring Martian Manhunter (with iconic being determined by what covers are most established and most recognized when it comes to Martian Manhunter, with a preference towards covers that are homaged a lot). This is not a BEST cover list and due to the very nature of icons, very few (if any) recent covers will be on the list. A notable exception to the rules is that I don't count covers from a character's first appearance (which isn't applicable to all characters, of course, just those who appeared on the cover of the comic they debuted in), as those tend to be automatically iconic so they're boring. Here's a list of all characters featured so far.
J'onn J'onnz is a tricky one, as he really has not had all that many covers - in fact, during almost the entire Giffen/DeMatteis JLI run, J'onn was, of course, a major part of the book and yet did not get a single cover spotlight until the very end of the run when it is a little hard-pressed to call it an "iconic" representation of J'onn's JLI tenure.
Artist: Howard Porter
Therefore, since he did not get any spotlights from the JLI, I thought it only right to note that early on, J'onn was chosen to be the JLA "representative" in DC's "Full Face" cover month (and yes, it was because he was the only one without his own title, but shaddup!).
Artist: Joe Certa
This was J'onn's first series that he starred in - you're a bit hard-pressed to pick ANY of these covers as iconic, but I felt it right that Joe Certa would have some representation on this list (and the other covers all featured J'onn's idiotic - and certainly NOT iconic as no one has really thinks of him as a major part of J'onn's history - alien pal, Zook)
Artist: Tom Mandrake
J'onn's first ongoing series where he was the only feature of the book (and got the book named after him, too).
Artist: George Roussos
The very first "two or three 'random' superheroes team-up" issue of The Brave and the Bold, and J'onn was one of the heroes featured!
Artist: Jim Starlin
Starlin almost got two covers on this list, as J'onn was featured on the DC Comics Presents cover that introduced Mongul, but really, it wasn't a particularly good cover for J'onn and nor was it a particularly historic event (no offense, Mongul).
Still, this was the first JLA cover that gave J'onn the spotlight, and it's a pretty cool spotlight at that (Starlin is riffing on the cover of Justice League of America #1, but I don't think it's an outright homage).
LAST COVERS CUT: J'onn's return to the JLA preceding JLDetroit had two sort of notable covers, the aforementioned one JLI cover that spotlighted J'onn (the one where he's looking out at Happy Harbor) and a cool looking cover from late in JLDetroit's run with J'onn on fire.