This is a problem that made me switch to Fedora for a while but I've finally found a solution for fixing Eclipse on Ubuntu and fixing the Aptana plugin as well.

The thing is that when you install Eclipse on Ubuntu it also installs GCJ and uses GCJ by default.

So you must do it like so.

If you don't have Eclipse installed go to
System > Administration > Synaptic Package Manager

type eclipse in the quick search. Check it

Then type sun java and check sun6-java-bin and sun6-java-jre

Then click Apply to install them.

Then go open a terminal from Applications > Accesories > Terminal
Paste this (you can paste in the terminal using ctrl-shift-v instead of the normal ctrl-v)
sudo update-java-alternatives -s java-6-sun

After that
sudo -b gedit /etc/eclipse/java_home

It will open the Text editor and you'll have to insert at the top

/usr/lib/jvm/java-6-sun

Remove any other line that's like that above
Save the file

Now eclipse should work ok and Aptana will not complain anymore regarding the need to use a certified Sun Java. Also it removed some problems regarding the Eclipse workspace that I was having.