If someone is sitting in that annoying open grave on the graveyard map, can that character be targeted by Pulse Wave or powers that can affect anywhere on the map (Shazam!'s Probability Control or Doom's special Outwit, for example)?

Pulse Wave is still a ranged attack, so no.

As for the other two, I'm pretty sure that'd fly.

I'd need to see the exact wordings, though.

Graveyard
Orange squares are hindering terrain for movement purposes and clear terrain for line of fire purposes. Any line of fire drawn to a character occupying an orange square is blocked.

View from Above: The Wizard Shazam! can use Enhancement and Probability Control. When he uses Probability Control, he may target a character anywhere on the map.

Lord of Latveria: Dr. Doom can use Outwit and Perplex. When Dr. Doom uses Outwit, he can use it normally, or you can roll a d6 instead; on a result of 4-6, counter a power possessed by a single target opposing character anywhere on the battlefield.

Well, looking at these, Pulse Wave is a no go as PW only ignores things associated with characters, not terrain. This is terrain or map features, ergo you are safe from PW

The other two do not mention any requirement for a LOF in their powers, just they may target anywhere. They are both good. Even though Doom's power says battlefield and WS's says map, they mean the same thing (though I fully expect someone to chime in that they are not)

PW would still hit them. PW states that it is only blocked by "these lines of fire are only blocked by walls, blocking and elevated terrain."

Does Pulse Wave override map write-ups? Sure, they ignore powers, but do they ignore the fact that you're HIDING in a hole?

Graveyard
Orange squares are hindering terrain for movement purposes and clear terrain for line of fire purposes. Any line of fire drawn to a character occupying an orange square is blocked.

Pulse Wave
...these lines of fire are only blocked by walls, blocking and elevated terrain.

Hmm, give me the map's stipulation then I play pulse wave and it says it isn't blocked by anything but those 3...okay, I'll buy that.

It doesn't override it. It's applying both and seeing which one controls. The Graveyard map indicates that any line of fire drawn to a character occupying an orange square is blocked. Pulse Wave indicates that the the lines of fire are only blocked by walls, blocking and elevated terrain. Since Pulse Wave lists the only things that block it and the orange squares of the Graveyard map are not on that list, Pulse Wave controls and the LOF is fine. (It's no different than Captain America's Deflection Trajectory.)