I have installed Aptana studio 3 and you can see the icon in Unity Dash is being displayed, very large.
Is it a Unity Dash bug or just Aptana Studio 3 bug ?
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This problem is due to a recent (not sure when) change in the way Unity displays icons. Aptana Studio 3 provides a .xpm file to use as the icon, which is what I'm assuming you're using. That's when this behaviour is seen and I've concluded that Unity can not resize .xpm images.
The fix is as simple as converting the .xpm file into a Unity friendly .png file that it can resize properly. You can do this online pretty easily at a site like http://www.convertmyimage.com/.
Once you get the converted .png file, make sure you update your .desktop file to reference this new .png and you should be all good to go.