Microsoft could be one example of a successful one. Their flagship Windows codebase that ran the 3.1->95->98->ME line was basically ditched with the rewrite-from-scratch NT (famously done by an ex-VMS team), which later had some APIs ported to it to make Windows 2000 and especially XP be close to drop-in replacements for the old line, while not really sharing much code. I think in retrospect that was probably a good idea: the NT rewrite put the codebase on much better footing than the aging, incrementally updated classic Windows codebase had been.
Solaris is another example of a rewrite that seems to have worked, though the rewrite did derive from a different set of existing code, not a total from-scratch job. But the classic SunOS 1.x.-4.x codebase was ditched, and SunOS 5.x / "Solaris 2" replaced it.
You covered Windows and Linux - don't forget Apple's switch to OS X. They wouldn't done a wholesale switch at some point even if they hadn't gone with something unix-based because the other alternative was Copeland, the internal project to do a complete rewrite.
Its a good point that NT was a successful rewrite. However, its worth noting how this was done. NT was originally aimed at a different market, there was a overlap of several years where the old system was still available AND NT ran Windows 3.1 apps in their own subsystem which contained .... the codebase of Windows 3.1.
I think the NT and OSX updates were absolutely required due to architectural reasons which impact security, 98/ME and MacOS 9 just simply weren't suited to types of threats on the internet (no support for dropping process privileges, file permissions, cutting direct access to hardware etc.). If you think XP is bad in 2010, think what Me would be like if widely installed still, one program crashing the whole machine, boot sector viruses etc.
Solaris is another example of a rewrite that seems to have worked, though the rewrite did derive from a different set of existing code, not a total from-scratch job. But the classic SunOS 1.x.-4.x codebase was ditched, and SunOS 5.x / "Solaris 2" replaced it.