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There is no such thing as a native UI for Linux because Linux has nothing to do with UI. As a kernel, it really only functions as a part of what you could see as a complete operating system.
If you want to have a native UI then you have to focus on the platform used for the UI, not just some kernel. Popular desktops that are used in combination with the Linux kernel on a GNU system are KDE and Gnome. I use Trinity. These desktops can work with different types of underlying operating systems, which may be interesting to support as well.
Instead of repeating myself too much I will refer you to the answer I gave to the poster above you. In short: my aim is one interface for each environment. So tell me what you use and how it should look and work there.
I use the Trinity Desktop Environment, which is basically a branch of an old version of KDE (version 3.5). You can find information about it here:
It is not shipped with any major GNU/Linux distribution (anymore/yet) and most people will consider its components outdated. It is still being used in many large scale desktop deployments however.
To get a fully native application for this environment, you would have to have it compile against all the outdated libraries that this desktop environment depends on. (Qt3 and kdelibs version 3.5.)
Because normally few people are going to develop their applications against these old libraries, right now there are development efforts from the Trinity side to get GTK and Qt4 applications to at least look as native. Using one of those two toolkits would be the safest.
I guess you already want to develop both a version targeted towards KDE 4 and a version for Gnome, so one of these versions should be relatively ok for Trinity as well. If you really do not want a to stand out at all, you will have to have a version that compiles against the Trinity libraries. Then it would be perfect for my environment.