Since some people already wrote a little bit about their favourite Gnome apps I also had a look at everything running in the daily live, and found, besides the usual stuff, an application I never found anything comparable in KDE: stardict
I use stardict mainly to translate form english to german while I’m reading difficult English texts where I just mark words which are then automatically fetched and translated by stardict with a passive popup – there is no additional window opening in front, there is no extra action I have to use, and so on. That is very helpful, especially if you want a quick, smooth solution for translating. I never found anything comparable (multilanguage, automatic running, etc.) for KDE.
The other apps are pretty well known: beagle is the first one which probably will not be replaced by anything else until KDE 4 comes out. Although it isn’t really Gnome it comes out of the Gnome corner, and I do prefer their search interface “beagle-search” over “kerry”. The other application I sometimes use is Gimp, but since the new Krita came out I switch now – Krita just provides much more functions and abilities, and although it will take some time to get used to the new program I will finish my switch quite soon.
I do not think that you will find a long time Linux user who really just uses apps from his preferred desktop environment – and why should you? Sure, we are still feeling the difference, and Portland/freedesktop.org and Tango has still a lot to do until we do not feel any difference anymore, but it is not bad at all, and shouldn’t be of interest for which desktop environment the program was designed – it was chosen for the features and the handling, and that should everything which counts in the end. It keeps alive the competition among friends which will crush other proprietary systems which do not have friends 😉