There are 3 options here.
1) use your server to generate a self signed SSL cert which is bound to your specific ip address and then run all your applications from this root IP address or make the applications appear that they run from it using relative links etc.
2) RECOMMENDED route:
setup a dedicated domain name such as yournameapplications.com and register this domain name with godaddy.com SSL certs. Godaddy are much cheaper for SSL certs than verisign or thawte. Run all your applications from this domain name using sub directories if necessary. This then chunks your applications up into their respective client directories, while maintaining SSL.
3) an alternative recommended route:
because of the really low cost of godaddy SSL certs (under $30 per year per domain), you could get your clients to register their own SSL cert for either their main domain or do a sub domain (apps.companyname-training.com) and run their secure application from there.
From a programming point of view, you could have the master php files (if they function the same for all clients) in a master directory. You then reference this master directory to the sub domain (apps.companyname-training.com) and check via code for which domain they are coming from to then apply the appropriate skin.
The benefits of 2 and 3 are that the SSL certs are signed by a world recognized certificate authority. Option 1 while free will throw up errors to each of your visitors saying that the cert is self signed and not authority signed. 30 bucks a year per domain isn't bad either when you look at the cost of most cert authorities.
Hope this helps.
P.S. I do not earn commissions from godaddy but wish I did for this purpose LOL. They are the best for the money and fulfill the need.