Jared,
couple more points here.
Not sure if Xandros has published the full text of the Xandros-Microsoft agreement - I believe not, but I would have to check; the interesting thing is that everybody talks about the patent part whiile the core part of the agreement is really about technology exchange and licensing, mainly integrating Xandros' and Microsoft's respective Systems Management infrastructure products and some protocol interoperability parts in areas where Linux-based Xandros solutions and Microsoft products coexist. Nobody has really commented about that part - it seems that most don't care with the exception of the customers that have been asking for more interoperable products for a long time, from both Microsoft and Xandros.
On the patent thing, if you check the news you'll find that this is not a mutual agreement, but Microsoft is just indemnifying Xandros *should* there be any infringements of Microsoft's existing patents in any Linux-based product published by Xandros. The protest of the open source community is that entering into such an agreement validates Microsoft's claim that Linux indeed infringes patent's owned by MSFT.
Now, if you want my opinion (and I'll add this time that this is my personal and does not necessarily represent the official position of the company I work for), it's drop dead simple. Yes, I am sure that if you are legally clever, you would find bits of code in Linux and related open source products that collide with patents held by Microsoft and other vendors. Period. The whole software world exists as a giant world of aggregation, copy/paste, implementing other peoples specs, doing similar or same things and otherwise. It's part of being in a completely networked world, of fundamental base technology (hardware) that only allows you to solve a problem in a finite number of ways and of people and technology exchange. A couple of Microsoft guys now work at Google, surely you can tell them that they may not use any knowledge from inside Redmond in their work, but (fortunately!), the MiB-type memory-eraser for our brains does not exist yet and the tagging of stuff in their isn't as good as on some tagging sites so that dangerous stuff can be filtered out.
Therefore, taking the 18th-century (and in some countries before that) concept of patents into the modern software world doesn't make any sense. There is a fine line between patents and simple theft of intellectual property, but the software world needs new definitions and new methodology. I am clearly against how the concept is currently implemented and I am happy that at least in the EU there is lots of fighting against it, both from the open source community as well as smaller software vendors. However, this is really a political questions and laws must be changed, etc. Until then, I really can't blame software companies large enough to do so for registering patents and at least trying to get some more legal peace of mind for themselves and their customers.
Now, commercial software companies seeking indemnification for their clients from possibly infringed 3rd party rights is nothing new. One of the cornerstones of Red Hat's Enterprise Linux is indemnification against unexpected copyright claims; what this means is that if any open source developer contributing to Linux or related technology is later found to be guilty of IP theft, assigning GPL-type copyrights to code that he indeed did not own and that would have made it into the distro, Red Hat would hold their customers free of any legal issues and subpoenas and whatever might occur as a consequence. They would just stand in, basically acting as a insurance that a customer would not have to shut down any of their systems or operations because of such claims, no matter what. In this case, Big Guy Red Hat protects their customers from Small Guy nonsense. Customers take such insurance and they need it - in sectors as finance, it is even obligatory to have them for business continuity reasons.
For me personally, as long as the patent debate around software is resolved on a political level, the patent thing is just about the same, only that companies are seeking to protect their customers from claims made by other vendors.
Yes, I do believe that some open source programs violate Microsoft's patents; I will make no guess on the number and the one published is most likely incorrect, tbut there will be some violations. Based on current (stupid!) law, this poses a risk to users of such software. In theory, companies like Microsoft could start trying to issue cease and desist orders for users of such technologies. Microsoft, unlike SCO, would most likely not do such crap, because the organisations affected are some of their best and most important customers and I don't think, Microsoft is actually stupid enough to cut that deep into their own meat. They, as you and I, also understand that the whole thing has no strong background.
IMHO, their only true fault is that they use the fact to create some FUD instead of being the really good guy, standing up, and help creating political pressure to clean this up; on the other hand, how can anybody blame them for that - the OSS community also creates quite a bit of Microsoft FUD and while some arguments against using the company's technology are valid and correct, some others are simply and downright wrong as well, so I guess this is normal stuff in the harsh and competitive world of being the largest software company.
From the viewpoint of some customers it's again very simple - certain types of technologies cannot easily be used at all for them (again, think finance or some automotive supply chain players) unless the legal situation is clean. They need insurance. IMHO, the Novell and Xandros agreements, at least on the patent side, are just that - insurance for the companies' corporate customers that certain things won't happen; it's the stupid type of insurance that we all believe we'll never need, yet still have to sign up for.
I firmly believe that this whole stuff will continue to go on - and might even include Red Hat at some point - until politics resolve the whole issue and that's where we should work. They've all done not-so-dissimilar things (think indemnification) in the past and if customers ask for it (and they do!) they will do it again.
I don't think coming to terms with someone on such a real issue automatically means jumping into a bed with them (at least that's not what I usually do - buying a car from a car dealer doesn't mean I'll sleep with her....

)
As for the GPLv3 part, I can't comment on that because the arguments get very hairy, legalesewise. For many useful and truthful comments, I would recommend Eben Moglen's wide body of work - he's been the legal counsel of the FSF for GPLv3, but afaik he's also adivsed Novell/Microsoft while they wrote up their agreement. The arguments whether any of these commercial agreements are in true violation of GPLv3 haven't been resolved to a point yet for me that it's clear what the actual outcome is. Now, my more important point here are the consequences; first, nobody would ever claim that an organisation entering a commercial agreement giving it patent protection (again, one-way), can no longer publish GPLv3-licensed software - it would only be where concrete patents and such software collide that there could ever be a problem. Second, I am not sure even Richard Stallman would agree if you said that only GPLv3-licensed software is True Open Source software; Scalix has published it's open source bits so far under a modified Mozilla License, like many others, and I understand the debate around that, but it's still open source software by any standards (I guess otherwise Firefox wouldn't be considered OSS) and it's not affected at all by any GPLv3 developments.
On the employee side, your analysis isn't quite right as well; Scalix's CEO, Glenn, remains on Xandros' advisory board and product (me myself

) and engineering management as part of the engineering team is still there, so it's certainly not about 'the brightest core engineers'. Presales technical people and services people are also still around and your comparison to those failed dot-coms isn't really valid IMHO, as those folks usually had some possibly interesting technology, but usually neither a business nor customers, where Scalix had - and has - both; I don't think any of the examples you're referring to would have showed up with a lineup of reference accounts comparable to ours.
We did lose a few people as part of the acquisition that we did not want to lose - part of that was pretty normal attrition for people having worked for the same employer for three, four years - sometimes you're just not in there anymore for internal organisational change. Also, the change of office locations has played a role here.
AFAICS, the Scalix group inside Xandros is very vital, on the development side we're in production mode and will publish a new release of Scalix before the end of the quarter. On the sales and marketing side, we'll be appearing at least in one major trade show in Europe in fall, have a couple of reviews coming up and I hope we've gotten our responsiveness to sales inquiries back to a normal level; at least I'm sure we're processing orders as I saw a good number coming in the other day.

I don't plan to struggle here, neither does anybody else. We've been too busy to truely celebrate, but everyone at Scalix I talk to is pretty happy about the new situation.
On your last point, I can't really comment; this is your business decision. What I can say is that going with Scalix at this point is probably as safe as with any 'small' Linux-based software vendor, including our competitors, with the difference that we now have the largest company wrapped around the product of all the other direct players in the same space. So I guess if you're looking for the no-risk product in this space, your only choice would appear to be Exchange...
Good luck,
Florian.