GPL version 3 paints Novell into a corner in it's "patent & interoperability" deal with Microsoft. (I'm assuming the GNU tools are early to upgrade their license from GPLv2 to GPLv3 and that the Linux kernel will certainly upgrade in time.)
The effects upon Novell's position of the terms of GPLv3 are quite simple to understand: Novell can either 1) elect itself out of the Linux business to protect its deal with Microsoft (something of a non sequitur); or 2) stay in the Linux business and thereby spread immunity from potential patent infringements to any customer who uses Novell's or any new GPLv3 versions of Linux.
(Among the layered ironies here, is that it is more likely that Microsoft is the infringer upon others' patents which may be contained in Linux.)
Holding aside the (greater) problems for Microsoft, the problem for Novell arises from the free-SuSE Linux support vouchers which Microsoft has been spreading around to its customers, making Microsoft a distributor of GPL software. In particular, the problem arises because the vouchers have no expiry date. With no end-date, the vouchers exercised by customers after GPLv3 code comes into use means that Microsoft, as a distributor, becomes subject to the terms of the GPLv3 license and therefore its patent license to Novell gets applied to all users of relevant GPLv3 code, not just Novell's customers.
This, according to the provisions of Sections 10, 11 & 12 (parts given below) of GPLv3, means that after Novell has upgraded the Linux kernel and GNU tools on its own development tree to GPLv3 code, then the resulting product will cause the same patent protections granted to Novell by Microsoft in their deal to be distributed to any "downstream" user of this code and other works derived from it. Thus, all users of Novell's SuSE and other distros of Linux after a certain time will have the same protections & immunities Microsoft attempted to grant only to Novell.
Accordingly, Novell can do one of two things: lose or lose...
In the first scenario, Novell can simply stop distributing Linux (not likely) or elect not to use GPLv3 code in its GNU/Linux-based products. This would mean Novell would have to effectively fork itself away from the Community activities and Community code -- away from GNU/Linux -- to become isolated as a lone steward of, over time, obsolete GPLv2 code. Ostensibly they would choose to do this in order to continue to honor the Microsoft deal, justify the large (company-saving) payment from Microsoft, and continue to "benefit" by being among the few commercial Linux vendors offering patent "protection". This scenario sees Novell removing itself from the Linux business to protect its vig from Microsoft. Yet, in the end, such a move would make Novell an uncompetitive and unattractive Linux partner. (The scenario is unlikely because it doesn't make business sense from Novell's perspective.)
In the second scenario, Novell loses a new uniqueness among Linux distributors it thought it had forged with the desktop Monopolist. Here, the company continues as normal to take down and work on the new GPLv3 code from the Community development trees of GNU/Linux and when any end user installs the resulting Novell product, they are subject to the immunity of the "patent license" granted by Microsoft to Novell customers; this occurs whether the case is an installation of the free voucher versions or of versions purchased from Novell. And here's the rub: the patent protections get automatically extended to all recipients of GPLv3 GNU/Linux code (see Section 11); the new terms nullify the Microsoft-Novell patent detente by spreading the protection to all GNU/Linux users & purveyors.
For Novell, the second scenario looks like the present course (this Novell has confirmed): the company stays in the Linux business, it stays current on GNU/Linux code and the only thing it loses is the uniqueness among Linux vendors as a source of protection against Microsoft's threatened legal lashings-out.
It would be easy to say this was a set-up by the Linux and the Free Software Communities against Microsoft; but it's been clear from triangulation in parallel and orthogonal experiences over time that Novell's senior people did not (do not) understand the GPL much better than Microsoft's. This makes the truth seem stranger than the fiction. But in the end it will be difficult to conclude other than that knowledge will continue to insist upon its freedom (this video is a rousing bit of oratory on June 26, 2007, from the homeland of Adam Smith by the Lawyer of the FSF).
For the curious and the other lawyers, here are the relevant parts of GPLv3, Sections 10, 11 & 12, on which I base my assertions. In particular, note how the license does not permit different terms to be attached by different purveyors to different recipients of the work...
Section 10 - Automatic Licensing of Downstream Recipients (exerpt)
Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License.
Section 11 - Patents (exerpt)
If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it (emphasis added).
Section 12 - No Surrender of Others' Freedoms (exerpt)
If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all.
Groklaw has an interpretation and discussion here, MS: Dancing as fast as it can to try to get away from GPLv3, which assumes some prior knowledge.
Microsoft can say it is not subject to the terms of the GPL, but one can say one is not subject to the forces of gravity...
This is likely to become a court case. If Microsoft can satisfy a court that it is not distributing Linux (via the support vouchers), then its present dissociation from Novell and GPLv3 might -- MIGHT -- hold up.