My favorite 3 (I always love your boy's lists, so hard to pick!)
Remus - One of my favorite HP charecters, Remus Lupin would be an awesome namesake. Also the Mythological roots ties it in really well with Aphrodite. (This is probably my favorite from the list if I have to pick a favorite)
Galileo - another great namesake
Sherlock - just because I love Sherlock Holmes, I'm not so sure about this with Aphrodite though, her being Ancient, him being more modern (couple thousand years versus a hundred or so)
Is Orlando now off the list? If he's not he would replace Sherlock in my top 3. I can easily imagine you with a son named Orlando, such a romantic name yet so masculine.
If I were to remove any from your list I would remove Herakules because he just seems so macho (and I like manly names,so it's hard for me to say a name is too macho), and Lancelot.
I just wrote you a novel on your girls thread, so I'll try to keep this short. Have I mentioned how much I love your boys'names? Have 5 sons! Lol
Galileo- wow. Just wow. If I ever met a boy named Galileo, I'd follow him home just to meet his parents.
Lucius- he feels like the male counterpart to Morgana. Does that make sense? That's how I see it in my head.
Orpheus- it's my husband's fave. He likes -us ending names. That's what he just said. Oh, and that a boy named Orpheus would be awesome. He doesn't give me much. Lol