A couple days ago I emailed Tor with some questions about Topaz and why they use it for some of their books. Today I got a reply from Pablo Defendini the producer for Tor.com. Since this has been discussed in a few threads I thought I'd share his message.
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I'm Pablo, the producer for Tor.com. I'm also charged with eBooks on Tor.com and am involved in the larger eBook strategy for Macmillan.
Unfortunately, there isn't too much we can do about Topaz books. I hate 'em too—they're a pain to parse on the Kindle, and will sometimes crash the device—but there's just some books that we don't have electronic files for, and the only way we can get them on to the Kindle at all in a speedy fashion is via Topaz files created from OCR'ed PDFs.
Going forward, we're obviously converting new books into AZW format directly, and hopefully we'd like to be able to rectify backlist titles at some point in the future. However, right now, our priority is our more recent books, as you can imagine. In the meantime, the people who actually handle these conversions is Amazon themselves. You might want to drop them a line and register your displeasure with the Topaz format. As I understand it, you wouldn't be the only one, and the more people they hear from, the more responsive they'll be, hopefully.
As to the store rumours: well, they're just that, and I can't talk about that for now. But I will be able to start talking soon, so stay tuned.
Cheers,
[p]
Pablo Defendini
Producer
Tor.com
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So all of you who are hating Topaz, be sure to let Amazon know.
When I replied to him that one of the books I specifically mentioned in my email,
Kushiel's Dart, had been a Webscriptions book so they should have a good copy of that, he replied...
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You'd be very surprised as to the state and consistency of digital archiving at a lot of major publishers, is all I'll say about Kushiel's Dart... 
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Hope this info helps or was able to answer questions for some of you.