Using Lego Digital Designer. So far I've got Mabe Village more or less done, which is where I originally planned to stop, but it's addictive so I might just carry on and see how much of the island I can do before I go mad.
Anyway, the village still needs a few tweaks, but here's the map so far- note the hideously not-to-scale Link, as I went with one 2x2 brick per tile, making doors (actually windows) about half the size they'd need to be for a minifig to go through
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"I'm Commander Shepard, and you're standing in the biggest library in Citadel Space. Look me up."