I have skills in Java and C#.
First I had a closer look at Java (Eclipse with Windowbuilder-Plugin). - Swing: But there is no natvie GUI-Support for GTK3 (e.g., HUD seems not to work)
Then I looked at JAVA - SWT: It is to heavy. I want do code a small app that improves the Ubuntu desktop. I don't want to ship a program with Eclipse included.
After that I found C# Mono (Monodevelop): GTK# is only for GTK2 available. A GTK3 port will come soon but is it possible to convert the program from GTK2 to GTK3 without extra adaptations? The next bad thing is, that Mono is now dropped from Ubuntu LTS 12.04. So I have no chance that my app would be a default app in an official Ubuntu live CD. (This is also a factor for me to choose a programming language).
I know there are other techs but I want to use as programming language Java or C#.
I would suggest not to dismiss Java and SWT on this basis. If you want something in Java that really looks native, SWT is your best option. Eclipse's WindowBuilder supports it will too. You're clearly misunderstanding what you need to ship with your application. You don't have to ship Eclipse, just the SWT jars. Unless you application is really simple, it's likely that you'll have to depend on 3rd party jars at one point or another (or ship your own anyway).
The main difference with Swing is that you need to ship the right SWT jar for the right platform (e.g. x86_64). It's not actually so hard to do, and can be packaged appropriately with a suitable build system.