Hello developers
This is NOT a question on what language is better, so NO flames please.
I'm quite into Java, in my life I tried a bit PHP, C/C++ and a few other langs. I decided to stay for now with Java, BUT, it doesn't have a good enough desktop API, yes, I'm aware of the new features from version 6, I'm exited about the new system tray functionality, OpenGL rendering, speed enhancements and lots of other features, however, I sometimes badly need to:
1. Let the window have different shapes (not the standard square)
2. Make my application's window (half)transparent
3. Interact with other running application windows -sending different events (in Window$ one uses the "find_window" function to find to find a window, and something like destroy_window to kill it (I've been coding for windows some time ago, so don't remember for sure), - there's no such thing in Java yet).
4. Make my program run at system startup (or when the user logs in). THIS is extremely important for me, as sometimes the application has to track some events, like alerting the user to do something planned or alike.
Java can't do this unless you bind it with C/C++ code (through a special mechanism) - so I have to write platform dependent code.. In such case I'd rather just use C and the native platform API, why would I bother doing it in Java..

So the question is: Is there any language that doesn't require recompilation when taking its application to another platform and which would allow any/some of the features above? I'm thinking of Python, C#..?
Please share your opinions

PS: One can use third party libraries, but still: 1. They are not part of the standard Java libraries so would need additional installation. 2. Not good enough to my mind..

The first three things you listed have directly to do with the X server, so you'd have to tie into the appropriate libraries to do so. If Java doesn't have these features, you can use the JNI to call into the right C functions. Of course, if you do that, such code won't be platform independent anymore. However, instead of relying on language you could rely on the toolkit to do this for you. I don't know of any that offer this kind of flexibility, though.

It does seem to me that point three could be accomplished by using multiple threads for your GUI. If you've got a different thread for each window, it would be easy for them to send messages to one another (assuming the threading style you're using supports the message-passing paradigm).

The last thing you list has to do with desktop environment (not the language). Gnome and KDE both have different ways of registering programs to run at session start. Windows has the startup folder. Under X you could just add the invocation to .xinitrc or .xsession.