Update: This whole situation ended up being resolved just a couple of weeks after this story was published, with HTC backing off on its assertion that the stock and custom HTC ROMs couldn't be distributed. It did request that the HTCRUU.com domain be handed over, but the ROMs that were hosted there previously will now be available at ruu.androidfiles.org. It's good to hear HTC isn't cracking down on the custom software community, though whether this resolution came about because of a legitimate misunderstanding, or simply as PR damage control, isn't clear.
It seems the days of centrally accessible HTC RUU files are at an end - for the time being - as the owner of HTCRUU.com was forced to surrender his site after a representative HTC's legal team suggested this was the only way to "resolve" his unauthorized hosting of HTC's software. No formal legal action was taken against the owner.
HTCRUU was quite simply a repository of Sense ROMs for HTC phones. HTC decided it didn't like that sort of thing, and told James his site infringed HTC's trademark and copyrights.
Which it did. It used HTC's logo, HTC's name in the URL, and it hosted proprietary HTC software, all without permission. Make no mistake - what James was doing was 100% in violation of HTC's intellectual property rights. But it's still easy to see why people may get upset about it.
HTC has generally left the custom ROM community to its own devices, apart from individuals who actively sought to publish unreleased HTC software. This has allowed a thriving Sense ROM community to emerge on XDA, RootzWiki, and other hubs of developer collaboration. But the shuttering of HTCRUU may be a shift to a stance of more active policing for the company.
The shutdown resulted in the removal of all files from HTCRUU, whether stock or custom Sense-based ROMs, and the eventual transferring of the domain to HTC (on grounds of trademark infringement). Any such files in temporary storage (eg, http://androidfiles.org/ruu/) must also be cleared out.