I have a Acer Aspire One, running its standard version of linpus. How do I delete files(programs I've installed via terminal) in the /opt folder. I don't have permission to do it via the file manager.

And more generally... how do I go about deleting any folder that root doesn't have permission to... for example, if someone was to alter the root's 'read and write' permission to 'none' how would I
a)Change it back to 'read and write' or
b)Delete it some other way.

You should be able to change the file permissions on any file as root using the chmod command. It is possible to use the chmod command as root to make a file read only even by root. If you want to later delete or modify that file you have to again use chmod on the file as root to change the permissions before you can delete the file even as root. You can determine the file permissions on any file by running:

# ls -l <file>

If you want to give the owner rwx permissions and all others rx permissions, run:

# chmod 755 <file>

To recursively change the permissions on all files in a given directory run

# chmod -R 755 <directory>

Root should then be able to delete the files or directory.

That worked well on the folder in my documents, I was able to change it back from no permissions and delete it. Thank you.

However it didn't work in /opt. But when I checked the permissions in it says the owner is '1000'. any ideas?

Thanks

As already stated by kilgoretrout, root should be able to remove any file or directory, despite its permissions (unless some extended attributes are set) and its owner. Even if the file/directory has no permissions at all, like
So the question is: are you sure you're running commands as root? Regarding your original question, if you installed some applications compiling them from source, removing the source directory does not uninstall the application, unless you explicitly installed it under the source directory itself. If you did not issue a make clean or make distclean command in the source directory, you should be able to issue a make uninstall, if the uninstall target is provided by the Makefile. Then you can safely remove the source directory and have the application completely removed.

If the problem is just to change the owner of the directory, use the chown command. For example:
will change recursively the owner and group of /opt/dir, being the name before the colon a valid username and the name after the colon a valid group name to which the user belongs.