Although it should be possible to create one partition that spans more than one physical drive, it's not a recommended path.
You are better off creating more than one partition, that just happen to live on different drives.
You want to use it as a server. Will you be using the home directories? Or will you keep most of your data in /var/www-data ?
Common paths to separate on different partitions are:
/boot -> this is often a separate partition, so you can use a different filesystem (grub doesn't support all filesystems)
/var -> this is assumed to contain data that changes a lot
/home -> this if often separated so you can easily reinstall without loosing user's files
/tmp -> this is assumed to have temporary data
Also, keep in mind you will need a separate swap partition no matter what you do.
I would put the swap-partition, and the /var partition on the fastest physical drive.
EDIT: Let's assume your fastest drive is the 40 gb one. In that case you may want to put /var/www-data on your larger drive, and just keep the root '/' and the swap on the fastest physical drive. This would mean you have three partitions: swap, / and /var/www-data. No need to separate the rest.