I have a server which is dedicated to one company which will have 2 or 3 physical sites on it. My problem is that the company has many domains which all resolve to the same site.

for example www.ddd.com www.ddd.co.uk www.ddd.org www.eee.com www.eee.co.uk all are the same website whereas www.test.com and www.test.co.uk would be two seperate testing sites.

There is no issue about ownership of the server or privacy issues between accounts on the server. I have been thinking about the best way to do this and have come up with a couple of scenarios:

1. Have the 2nd and 3rd sites defined in Plesk with the main site in the default structure. This would allow me to have the DNS entries point to the server ip and they would all pick up the correct web site from the default server. Downside of this is that it isnt then managed within Plesk, and what happens with the email sent to these accounts?
   
2. Have a "main" domain account set up and then modify the hosts.conf file to include all the domains that the Virtual Server will host. Downside is that the hosts.conf file is overwritten by Plesk each time the configuration changes.
   
3. Have a "main" domain account set up in Plesk then add the other domains using the vhost.conf file and defining the additional domains in a seperate tag

In all cases it is a little unclear what will happen with the email from the various additional domains.

Which option is the best, or is there an other solution that I have overlooked?

Writing without looking at my server, so bear with me... If you go to the plesk directory on your server there should be a dns folder in there and under that there is a file named.conf and under /var/ there will be files named domain.com, domain.org that have the dns information in it. From what you are describing you should only need one site in plesk, and you can make the dns changes manually so all of the other domains resolve. You will probably have to make manual changes in Apache/IIS as well.

I'm not 100% certain on the email part of it, as I'm thinking domain.co.uk probably can't have an mx record that says mail.domain.com. You're looking for email to work on any domain but only have one actual mailbox per user instead of 2 or 3 or whatever?

Create all domain on your server
install the main domain
do a simlink of the httpdocs/ on all other domain

i think its the easyer, but not tryed it you can give a try..