I'm running Ubuntu, Intrepid Ibex, and downloaded the 1.40.deb file for linux on the web site. I followed the instructions on the forum to install the game on ubuntu. The first direction it gave was:

Enter: sudo apt-get install ia32-libs to install 32-bit compatibility libraries.

To which I got: "E: Couldn't find package ia32-libs"

I finished installing the game and it seemed to install okay, it runs fine. But it won't autosave, and asks to create a new profile everytime I start the game again. I've tried re-installing it, but it changed nothing. I don't know if it not finding the ia32 package matters or not.
I've been searching the forum, but I haven't found a solution. If anyone could help me, that'd be awesome.

Check you can write to the ".WorldOfGoo" directory in your home directory. If you ran it first as root, you might have to fix the permissions.

Are you using a 32-bit or 64-bit version of Ubuntu? In the first case, you don't need to bother with ia32 libraries at all; you should be able to just install the package normally (e.g. save it on the desktop, then click on it).

Secondly, the per-user configuration goes into $HOME/.WorldOfGoo/ as davidc pointed out. Could you open a console and print the output of entering ls -la $HOME/.WorldOfGoo/ ? Could you also post the contents of $HOME/.WorldOfGoo/WorldOfGoo.log, if it exists?