Currently, many of our modules have no .install file, yet they set Druapl system variables that would get left behind in the database if the module were disabled/removed. Adding this function to an existing .install file, or creating a blank .install file with just this function will remedy this. If the .install file already has a hook_uninstall() function, check the code to make sure it does something similar to this funciton to clean up its variables.
This works for version 5.x and 6.x modules.
modulename.install
<?php
function modulename_uninstall() {
$vars = db_query("select * from {variable} where name like 'modulename%'");
while ($var = db_fetch_object($vars)) {
variable_del($var->name);
}
}