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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It is not shipped with any major GNU/Linux distribution (anymore/yet) and most people will consider its components outdated.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To get a fully native application for this environment, you would have to have it compile against all the outdated libraries that this desktop environment depends on.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.
Let's assume there will be only one version of Stoffi: A Trinity version. Let's also assume that I will be able to find out myself where to use drop shadows, the fonts to use, button gradients and so on. What other things should I consider? Do you have tips on some applications on Trinity from where I should draw inspiration? Should I go for a menubar or not? Should I keep the current layout (left=navigation, top=playback, bottom=information, right=content) or should it be something else? What should happen when you press minimize or close? Should it close to tray or not? How should preferences be structured? If there will be a menu how should it be organized?
These are the smaller details that I think are absolutely necessary to consider when trying to make a version of Stoffi that feels like it's actually a part of Trinity and not a third party application.
I guess you could look at the Trinity version of Amarok to find most inspiration for your application.
Your layout seems ok to me, but for me, any layout would feel equally native to me. It's the appearance of the widgets and the speed of the overall application that would make the difference.
I guess minimize should minimize to the taskbar and close should be configurable to either close or still keep it running in the system tray (that would be the default action). This is how other programs have it in Trinity.
For a native Trinity application, there will almost always be the possibility to have a menu-bar, but it can also be turned off. In addition there is a configurable toolbar (large/small icons, text/no-text, button layout, etc.). It depends on whether your application really works easier with a menu bar whether it's enabled or not by default (in most cases yes, only a few no).