I've recently just did it.
The following sites:
https://www.DNNReactor.com
https://www.Rad-Websites.com
and
https://www.MusicianHouse.com
are all runnign on the same instance of DotNetNuke on one server, using one SSL certificate for all three. SSL really has nothing to do with DotNetNuke so much....each page can be SSL or not, with a click of a mouse in DotNetNuke. The snag is in IIS.
Now in a scenario like this, there is only one downfall that I can see off hand. I use GoDaddy for my SSL certificate, and even though it's valid on all three sites(actually up to 4 or 5 I can use this cert on), the "site seal" that godaddy gives you, only shows the first domain name, so on www.rad-websites.com if I had a site seal installed, it'd still say www.dnnreactor.com
Take a look at this page: http://www.musicianhouse.com/Buy/tabid/1169/List/0/Default.aspx
On the left pane, bottom position, you'll see the godaddy site seal, and it tests valid and safe, but everything points to another domain name(dnnreactor).
So, if planning to use a "site seal" on the sites, I'm not sure what sort of "sense" that gives the end user who's lookign for a sense of security...But, the site loads up in IE, or any browser I use, secrue, with no warnings or errors....so if your not using a "site seal" on your site to give people a cozy feeling, then there is no issue doing it this way at all..
Back to it, you generate your new SSL cert request in IIS, save the text, go over to godaddy, and buy the....."Multi Domain UCC" version of the SSL certificate. They have very detailed instructions on how to install it on your IIS and it' goes very smooth. They have different "extras", I just got the "standard SLL" package, with multi domain support. you have to look at your case and determine where you fit best.
install it, and whatever sites you have associated to that Multi cetificate, will work, no problem, secured in DotNetNuke, when you set the checkbox under the host menu to allow SSL.
Now, on the negative end, any sites that decide, on that instance to use SSL, but are not assigned to the certificate on godaddies end, willl go secure, but give so many red lights and warnings to the end user that they can't even figure out where your site went :->
Anyhow, once you do it one time, it's really simple, but the first time can be confusing and seem more intimidating that it is. If you want, go to one of my websites, I guess DNNReactor is the best place, register wiht a valid email address and post me in the forms that you want me to help you and I will...no charge. I'd say just email me at "blahblah" but I don't like robots that grab my email address and start spammign me :->
Anyhow it's easy, let me know if I can help, I'll walk you through it over IM, email, phone, whatever.