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"A number of minerals crystallize in the cubic (isometric) system and some of them form nearly perfect cubes. One of these is iron pyrite (iron sulphide) -- a likely candidate for this situation because it can be easily dislodged from its host rock matrix or chemically degraded. I've found square holes in rocks where pyrite crystals were formerly located. But there are other cubic minerals that could do the same thing." Interesting that you brought this up. I have been looking into some interesting information that is a theoretical possibility for this hole. First off. Olivine is well known to be present on mars. Now olivine disolves easily in water and if indeed this was a lake bed the it could also explain how a an isometric olivine crystal (obviously megacrystic) that could have formed in the mantel and exposed to water could have disolved away completely or enough to have fallen out of the matrix rock. Here's the articles on the presense of olivine: The first link is good reading on locations of olivine from TES images and the second is the explanation of the formation of isometric olivine in the martian mantle.
http://www.psrd.hawaii.edu/Nov03/olivine.html

http://www.nd.edu/~cneal/eg.101/geology2/geology2.html
Specifically go down to the heading called Expansion of the Martian Mantle to see how isometric olivine occurs on mars. It's possible we could be on to something here... Appearance of this rock look similar to basalt? Certainly darker...

Olivine's interesting -- I have a metallic meteorite specimen that displays large included olivine crystals. It's fascinating. So are your links.

Olivine is the same as the gemstone peridot. It's usually associated with volcanics like basalt -- in fact it's the only gemstone found in Hawaii. But I'm only familiar with the type that crystallizes in the orthorhombic system.

At first I was going to discount olivine as a possibility but the information about its ability to crystallize in the isometric system under certain conditions -- something I didn't know -- made me think again. You've done some serious homework here! That, combined with the spectroscopic evidence in the first link, could make an interesting case for olivine. Of course we're not sure the dark area is a hole yet. But it's loads of fun to speculate.