In 2006, Microsoft posted a high-level summary of 235 patents that were allegedly violated by free and open source software (Foss), including the Linux kernel, samba, openoffice.org and others. Shortly after that, MS entered into a series of three contracts with NOVELL, one of which was a patent agreement that said, "don’t sue us and we won't sue you"
At the time of this scenario, some dire consequences were predicted for Foss. This is how Foss has fared since then. Well, Linux is still alive and active, and all of the products you mentioned are still active as well.. Overall, I'd say open source software is still going strong, with no signs of stopping in the near future

The impact that those events have made since then, or possibly make in the future are.
The claim of Microsoft patents in Linux surfaced in 2004, when Ballmer misquoted a Pub Pat study and claimed Linux violated 228 patents. In 2007, Microsoft followed up telling Forbes that Linux and open source violated 235 patents: 42 in the Linux kernel, Linux graphical user interfaces violated 65, Open Office 45, various free/open e-mail programs violated another 15, and assorted, sundry free/open-source software programs violated 68 Microsoft patents.

Since then, Microsoft’s been diligently squaring away patent protection and licensing deals with Linux companies. The starting point, and summit, was the 2006 deal with Novell.

Tom Tom has been a long time coming. It is still not known how the tom tom lawsuit will come out According to Microsoft’s complaint, tom Tom either took the Red Hat road to signing Microsoft patent protection licensing deals and decided there was no case to answer or wouldn’t agree to Microsoft’s terms. Among its claims, Microsoft is seeking damages from tom-tom.

Whatever the merits of Microsoft’s case, and no matter how much Microsoft has insisted “this is not about Linux,” the case will erase hard-won gains Microsoft’s made in the open-source community. The noise storm that’s coming will overwhelm progressive voices in Microsoft’s open-source team and poison the atmosphere they must enter at events like EclipseCon and the O’Reilly Open Source Convention (OSCON).

That’s important.
The question of whether Foss has been helped or hurt, or neither. Free software is great, and corporate America loves it. Looking through many articles, I don’t believe the threat of a lawsuit had any impact on the free open source market at all. People will continue to download just about anything these days. FOSS has good quality codes that can be changed, shared, copied at will, and downloaded. It's versatile - it can be customized to perform almost any large-scale computing task and it's pretty close to being crash-resistant. A broad community of developers, from individuals to large companies like IBM, is constantly working to improve it and introduce new features. (Parloff, 2007)
What has changed since then Microsoft, who has become a strongly pro-software patent company (despite Bill Gates' old claim that patents would have harmed the software industry in the early days), is finding out (yet again) that such a stance can come back to bite you. We've already covered the somewhat ridiculous lawsuit that Microsoft faced from a small Canadian company, i4i, who claimed a patent (5,787,449) on an XML editing feature. Microsoft lost the lawsuit, and the court issued an injunction against Microsoft and claimed that the feature was worth an astounding $98 per copy where the feature was used. Microsoft appealed the case to CAFC who upheld the lower court ruling. Microsoft then appealed to have the entire CAFC rehear the case, and that got rejected. The only move left is to appeal to the Supreme Court that's exactly what Microsoft has now done.

To be honest, I can't see the Supreme Court actually taking this case. Unlike some of the other patent cases that the Supremes have taken recently, there doesn't seem to be any big constitutional questions here. It's just a silly patent that Microsoft is on the hook for infringing. Perhaps rather than fighting this individual battle, Microsoft will finally realize that it's stance on patents is only going to do it more harm in the long run.