I used to have Eclipse 3.5.2 working from my Limited User Account (i.e. not Administrator).
But when I upgraded to 3.6.2, Eclipse refuses to run in the Limited User
I wouldn't chmod to 777 to fix this problem. In my case the owner was root:root after a Rational Team Concert install for some RTC files and not my userid. Go to your user's home directory and ls -ltr to see what your userid and groupid are (on Ubuntu mine were both the same) and then execute the following on your eclipse subdirectory
sudo chown -R myuserid:groupid /opt/ibm/eclipse