here is what I did in a similar case.
Let's say you have 2 websites with 2 store view each. both website have a EN and a DE store view (codes can be anything).
First create 2 folders in the root of your magento install with 2 subfolders each.
Then copy index.php and .htaccess into website1, website1/en, website1/de. Do the same for website2 and its subfolders.
Now edit index.php from all the folders and subfolders like this:
website1/index.php and website2/index.php
replace $mageFilename = MAGENTO_ROOT . '/app/Mage.php'; with $mageFilename = '../app/Mage.php'; and
Mage::run($mageRunCode, $mageRunType);
with
Mage::run('website code here for each website', 'website');
Then in the index.php of each of the de|en folders
change $mageFilename = MAGENTO_ROOT . '/app/Mage.php'; to $mageFilename = '.././app/Mage.php';
and
Mage::run($mageRunCode, $mageRunType);
to
Mage::run('each store view code here', 'store');
Now remove the Show store codes in url flag.
In System->Configuration->web->unsecure set the these values
Base Skin URL : http://example.com/skin/ instead of {{unsecure_base_url}}skin/Base Media URL : http://example.com/media/ instead of {{unsecure_base_url}}media/Base JavaScript URL : http://example.com/js/ instead of {{unsecure_base_url}}js/
Do the same for the secure section if you are using secure urls just put https instead of http.
Now you have to create 2 virtual hosts, one for each website.
The document root for the first website will be website1 folder and for the second one website2.
If you want you can create only one folder website1 but this means that you have to create the en and de folders in the root folder of your magento instance for the second website and your second website has to have the document root, the root of your magento instance.
