I had both Eclipse and Aptana installed on the same machine without any problems. I now have Eclipse and NetBeans on this machine, and I know that they do not interfere with each other in the least.
I also had different versions of the same IDE (NetBeans) installed on the same machine, with different versions installed in different directories, and even this did not cause any problems. You can even list them in the same project folders if you want.
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