I was a HTC fanboi (and still sorta am), but most mainstream HOX vs SGS3 comparisons have resulted in a tie with each phone winning some of the major categories. Coming from a HTC Thunderbolt, I went for the SGS3 this time. Here's why:
The HOX wins in screen architecture and camera, hands down. SGS3 wins in storage, battery life (almost double when doing intense tasks like gaming and HD video according to Engadget and several other reviews), and RAM. Processors are plenty fast in high-end Android devices right now and most apps don't even utilize quad-core yet - and from what I've read the Krait outperforms the Exynos in single-threading tasks anyway. RAM is the bottleneck these days and the main reason for phone sluggishness right now so 2 gigs in the SGS3 has "win" written all over it.
Plus if you're a rooter/custom ROM kind of user, Samsungs have been more friendly in the bootloader world these days. There is no S-Off with the HOX right now unless you use HTC's unlock tool (which isn't really even S-Off) which voids your warranty - HTC DEV unlock requires you to input your serial number that is added to HTC's balcklist - in this regard the Sammy is the way to go.
I still love the competition between HTC and Samsung these days which is forcing them to push the envelope, and I fully intend to buy another HTC in the future. But today Samsung is my choice