The best desktop environment regarding consistency is BeOS, hands down. Because of the (double-edged) sword of not having other toolkits ported to the BeOS and because the guidelines were quite clear on the way things should work under BeOS, you get a very consistent (and simple) environment all the way through. The only other real toolkit ever created for BeOS was LibLayout, which was always very BeOS-ish anyway (except the tab look). Preference panels and even applications share a common behavior, look and feel. They do what you expect them to do (the BeOS way).
As for Windows, It is great to be able to run old Windows software under Windows XP, but that doesn't always mean that you will get same look and feel and even behavior throughout all applications (example: PaintShopPro 5's old Save/Open dialog). Additionally, Microsoft has introduced different behaviors on their own products, notably with MS Office offerings, toolbars are more flexible on IE than on other apps, while the .NET apps have a dual look. However, control panels, dialogs, preference panels and all "default" tools found on Windows all follow the Microsoft HIG, so that is a plus.
MacOSX has three main toolkits to play with and while there are a few small differences between Carbon and Cocoa applications, all in all, OSX is very consistent with itself. However, not everything is roses here either. Apple has decided to go "wild" regarding the metal-looking applications like Safari, iMovie, iTunes etc which do create inconsistency to the whole experience. Mac OS X users have written down their complaints about this and other issues. A lot of people though still need to run special MacOS 9 applications who have the old look, so that doesn't help the current consistency either...
Hmm... Gnome and KDE... Well, it is impossible to say that any of the X11 environments are consistent. By definition they are not. Maybe they are consistent with themselves, but not when counting the whole experience. Even for people who run KDE and don't want to run GTK+ apps, there are so many other toolkits under X where every now and then you have to download and use an application that only exists under another toolkit (e.g. Motif or Tcl/Tk). Also, the brand new commercial ports of Moho, TextMaker and Pepper also are using... their own toolkits in order for their port to happen easier. The most important free applications under Linux today are also not consistent with the two main DEs: OpenOffice.org and Mozilla. All that adds up to the overall inconsistency of the X11 environment. And we haven't even mentioned the original Athena widget set, neither the different looks and interface layouts we get from important applications that are still available only as Qt 2.x (e.g. Opera) or as GTK+ 1.x (e.g. AbiWord, Gnumeric, GNUcash and many more).
Additionally, we get Qt applications that have different open/save dialogs than KDE's... We also get big Gnome applications that don't follow the Gnome HIGs (e.g. BlueFish 0.9). Surely, badly designed applications can be found under any operating system, but the main applications for the other DEs are HIGified and usability-tested, something that doesn't happen often for the main third party apps of any X11 environment.
Rating: Windows XP 8.5, MacOSX 7.5, KDE 5, BeOS 10, Gnome 5.
For me, integration is one of the most important aspects of a desktop environment. The reason I use a graphical desktop environment in the first place is to hide the complex aspects of the under-the-hood system and provide me with tools to configure the system, if and when this is required.
I found that the best DE on integration (see: the DE that requires you LESS to open a terminal window) is Windows, hands down. Everything can be configured with a GUI and when there is not a preference panel for something, there is always... the registry, even when you want to enable the most weird hacks on applications found or your system.
After XP should be MacOSX. A lot can be done via the GUI and via the NetInfo Manager or other utilities found on /Applications/Utilities. Great stuff.
BeOS is very good on abstracting the complexity as well, but it doesn't offer too many tools (though there are third party tools for such operations and also is easy to add more, as BeOS is a solid and simple system as we reported above). There are times that you will need to open a terminal to do things, like checking the integrity of the BFS, the makebootable utility, lsindex etc. Overall, this doesn't look bad for BeOS, just because working with that system is simple. But if BeOS was a Unix, the lack of more utilities would be more glaring.
Both KDE and Gnome include some preference panels to configure their own UI aspects, but none of these X11 environments are integrated to the underlying system. Maybe because X11 itself is not integrated, but runs "on top" of whatever Unix carries it. The good thing about it is that you can have choice of different DEs and that you can restart X when something becomes screwy, but in my opinion the bad stuff overwhelms the benefits: non-optimized X11, slow window manager architecture and more. Additionally, both Gnome and KDE don't offer tools to change the native resolution of X (this will change soon though, but it should have been here years ago already), no tools to configure internet connections, startup OS items, a GUI to load/unload/install/uninstall drivers on the fly [or by rebooting], no GUI on configuring printers/scanners/other hardware. Gnome and KDE feel more like shells, and while this is what they really are if you clearly look at them, they don't solve the given problem (even if they never meant to, it is irrelevant here, as the overall experience is what matters). Integration is the main key for an OS to feel mature and professional, but because of the multi-platform nature of these projects, it is not possible at this time. Most Linux distributions offer their own additional tools on whatever else is needed, but I don't get these extra tools with Solaris and Gnome, or with IRIX and KDE, and certainly not with FreeBSD or AIX. You might think (and rightly so) that this is a job for the OS provider to add more tools, but the fact remains that Gnome and KDE are far from integrated to any OS they run on and that does have an impact in the experience.
Rating: Windows XP 10, MacOSX 9, KDE 4, BeOS 8.5, Gnome 4.
I think that Mac, BeOS and Windows have roughly the same amount of flexibility in their UI. They all follow the philosophy of "less is more" and the OS provider just tries to provide the best defaults. You can change a fair amount of things, like position and size of the taskbar, but overall, the experience remains similar to the default.
Gnome is also like the bunch above, but it is more flexible in the way you can play with the way your Gnome panels look and behave. On the other hand, Gnome does not have a proper menu editor and modifying or creating new desktop shortcuts is a pain, going through all those tabs in the dialog box for such a simple operation.
KDE is the most flexible of all. Literally, every modification you can think of is possible there (expect automatically resizing kicker when more apps are sitting on its taskbar and Kicker is aligned in the center of the monitor like OSX's Dock). However, this flexibility comes at a cost. The Kontrol Center of KDE is just bloated, plain and simple. It is impossible to easily find the most common options which are under tones of other mostly insignificant or nit-picking options. There is a huge list of options on the left of the GUI application of KCenter, and on the right you get the selected KPart application with a number of tab views which each one has a number of options to explore. Some say that this is the very strength of KDE, but for me and others, this is a plague which results into confusion, usability and bloat headaches. I give KDE an 8 (and not a 9 or 10) because of these problems created by this flexibility, not because the flexibility is not there (it is).
Rating: Windows XP 7, MacOSX 7, KDE 8, BeOS 7, Gnome 7.5.