See the title – are there any show-stopping differences between GNOME and KDE, at this point? Is it just a matter of preference? I know some applications run 'better' one or the other, but besides that, are they each geared towards something specific?
Linux – What are the differences between Linux Window Managers
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Ok, let's try to make it short and not get into an (ugly) troll.
GNOME is the most common environment currently (let it be known: it's not mine ;)). It uses the Gtk graphical set (for Gimp ToolKit, since it was created for Gimp initially). The main idea behind GNOME is close to the idea behind UNIX systems generally: one program = one function. Each program has a specific use, and programs generally don't try to do more than they should. It is quite common that programs implement their own way of managing data, too. As far as style is concerned, people who don't like GNOME usually dislike the look and ergonomy of its dialog boxes (open/save/etc.)
KDE is another very old desktop environment. In fact, GNOME was originally created to replace KDE because KDE is built upon Qt (as a graphical toolkit), which was not open-source at the time (but now is). KDE is a huge, unified project, which has quite a different approach from the GNOME project. Many programs in KDE do quite a few things. It is not rare for KDE programs to get quite big and multi-functional (see Konqueror for example). Some like that, some don't. People who don't like KDE usually say it looks & feels too much like Windows (it really depends on the style/theme you apply in fact) or it looks childish. KDE has changed a lot in the last few years with the release of the KDE4 series, which is still a bit unstable (compared to what KDE3 used to be), but got quite usable with since release 4.3.
XFCE is a lightweight (although not at all the most lightweight) environment. Xubuntu was initially created for old machines that couldn't run GNOME or KDE properly. XFCE uses Gtk just like GNOME, and quite a few programs from Xubuntu are actually the same as in Ubuntu, or sometimes lightweight versions of them.
In general, it is better to avoid mixing environments, not because we're just extremists people who choose a side and don't depart from it, but because it loads more graphical libraries each time (Gtk and Qt mostly). As I said, KDE is generally a more unified environment, so it also pulls more dependencies between programs, which means installing a KDE program in a GNOME environment might make it feel quite heavy when all the KDE libraries load for just one program, while loading a GNOME program (such as Gimp) inside KDE won't be so heavy since Gtk programs don't interact as much as KDE programs do. I run KDE and I don't care to load Gtk programs when I (really) need, but GNOME users often complain that KDE programs slow down their desktop experience.
In the end, it's about where you feel best after trying a few of them (you might also consider E17 and openbox, for the fairness of mentioning these other famous environments).
To my knowledge, window transparency is the job of the window manager. I'm pretty sure--but someone please correct me if I'm wrong--that the only way to accomplish this is by using a window manager, such as Compiz, that supports transparency.
How come you don't want to use Compiz? If you're just trying to avoid Gnome and KDE, you can use Compiz independently of your desktop environment.
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To add to what Nikhil said:
Well, I think one of the main things that differentiates KDE and GNOME in particular is that GNOME is aimed at making things easy and straightforward, at least from their point of view (I say this because there have been many arguments amongst the developers from both camps as to what is 'easy and straightforward'). KDE on the other hand seems to give users a lot more options. What's interesting is that if you're in any way comfortable with computers, it might end up being that KDE, with its more options, would seem easier for you since you have more possibilities in terms of customizing things to your liking, whereas on GNOME you might be wondering where or how you do a certain thing.
But yeah, I think the only difference is the ideology and goals of both projects, and whether or not they match your way of working or perception of using a computer. Nowadays, programs written with a particular Desktop Environment over another still seem to work fine on the other, so it really does seem to come down to personal preference.
I personally have gone back and forth between the two, but I believe I've used KDE when I work as it feels a lot more versatile, in my particular experience of course. For simple browsing and computer usage, GNOME feels comfortable and easy.