This is very good! A few more of my own points I suppose...
This picture of the castle town centre is obviously influenced in a Graeco-Roman fashion with those porticos.
In addition, note the Temple of Time as well:
This is clearly inspired by the Roman Pantheon, as the picture explains. In this room we also fight this guy:
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Oh, hello there Achilles!

I doubt the darknut is meant to be Achilles himself, but the darknut is reminiscent of traditional Graeco-Roman military armour, no?
In fact, the whole of the Past-Temple of Time in
TP is heavily influenced by Graeco-Roman architecture...

Note the wall carvings, they were very common in the classical period. They appear throughout the dungeon.
In fact, the Temple of Time even in
OoT has some semblance to a Hellenistic temple:

Throughout
OoT we see a lot of references. The Forest Temple is particuarly good:
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Obviously this is a pediment, a feature of classical architecture. Note also the artwork for the temple too:
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Also the place has a rotunda, another feature of classical architecture:

Furthermore, the ferry in the Shadow Temple, that is distinctly reminiscent of the River Styx. See the article here for more information:
Styx - Wikipedia, the free encyclopedia and in particular Charon, who would ferry those to the underworld:
Charon (mythology) - Wikipedia, the free encyclopedia
Playing the Wind Waker, I also thought of the Tower of the Gods as being a little like the Lighthouse of Alexandria:

Not exactly, I grant you, but it's a long shot.
Finally, hey, what about this too?
Not all victims of crucifixion were crucified on a Latin Cross (the one Jesus is pictured as dying on) and it is fair to say that this type potentially could have been more common....a little gruesome eh? Nice thought for you to finish on...
I've got lots of ideas but probably too many for a single post! In my opinion I see Hyrule as being a little like Italy and the Roman Empire...but then I am a classics geek...