That's odd. I find Gnome apps mostly consistent and the occasional differences are there mainly when it makes good sense to be different. Not to say there is no occasional weird app that is less than usable, but, for the most of my time, they all get high marks.
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Yes, BUT, _that's within Gnome_. Gnome is a unified desktop environment of sorts. If you go outside of that (or KDE, XFCE, etc.), things are more ad-hoc. Some things use GTK, some use Qt, some old stuff uses Athena widgets, etc.
While using Vista, one experiences programs that expose Vista controls. Some others show XP-ish controls, while some others still look a lot like Windows 95/98/2K and, still, there are others that break away completely (Office 2007, Nero) and present a completely different user interface with weird shaped windows and menus that look like nothing else in the OS.
OSX is somewhat better organized, but, still, programs, even Apple ones (Safari? iTunes) have a variety of looks that get presented without much coherence. Apple is too guilty of this.