For some reason, the icon that IDEA provides to the Window Manager on Linux is not the best one - it is of low resolution and is not transparent, see the screenshot. Both icons provided in the tar.gz by default also have this problem (idea16.png and idea32.png) - they are pngs, but without the alpha channel. Some time ago I was able to find a very good idea48.png from one of the jar files (can't find it now). I think that this icon should be the default one to make IDEA look pretty on Linux, just like it is on a Mac