Certificates Concepts
Certificates - All you wanted to know about them
Self signed certificates
The certificate created by sme by default is a self signed certificate. That means it is issued by sme server and as such has not been tested or authenticated by any external certificate issuing Authority eg VeriSign & others etc.
This also means that the root certificate which is installed in most browsers by default (so the browser knows about all the commercial certificates and happily accepts them), does not know about the sme server self signed certificate, and therefore a web browser does not trust the certificate that is presented to it when a user tries to access a https site on your web server.
Therefore the users must install the self signed certificate into their browser the very first time they access your web server using https. After that they will not be asked again when they next access your site using https, as long as they are accessing from the same PC/browser. The problem is that with current generation web browsers, they issue very scary warnings that can put off many people and make them scared to access your site at all, and certainly reluctant to install a certificate about which they are being given a security breach type of warning.
There is another issue here, you should advise users to browse to https://servername.yourmaindomain.com/webmail (for example) and that name will match the name on the self signed certificate issued by sme server. That at least prevents name discrepancies, but still does not avoid the need to install the certificate on the very first https access.
Obviously external DNS records have to support that URL ie you would usually setup a wildcard in external DNS records that makes *.yourmaindomain.com resolve to your server IP.
Commercial certificates
If you use a commercially available certificate & pay money for it, the organisation who issues the certificate pays big money to Microsoft & Mozilla etc to have their root certificate installed in the browser by default. That's why if you use a good quality commercial certificate on your server, then when a visitor to your site accesses https://.... , they will not be asked anything about the certificate mismatching or not being installed etc, as the browser already knows that certificates from say VeriSign are legitimate and happily accepts the connection without question, as it is already trusted. Same for other major brands of commercial certificates.
Freely available certificates
If you choose to create your own certificate using one of the Howtos eg the CACert Howto, then the first time visitors access your site (https), they will still get asked to install the certificate into their browser. This is because CACert does not pay Microsoft $10,000 or more regularly to have their root certificate automatically installed in Internet Explorer (& updates which also update the root certifcate) etc. The same goes for other major brands of web browsers, although work is progressing to improve the relationship between CACert & other free certificate issuers and various web browser authors.
You can refer your visitors to the CACert website and get them to install the CACert root certificate and they will no longer be questioned about the certificate on your server, as your CACert certificate is now trusted by their browser (as it has the CACert root certificate installed). You can go either way really, get users to install your CACert certificate or get them to install the CACert root certificate.
You will still have renewal issues with CACert certificates for example, as they are only valid for 6 months, unless you join the special recognition program and show proof of identity to a authorised human being in your area, when they are then valid for 2 years. Ultimately at some time in the future, you will need to renew the CACert certificate, and install that new certificate onto sme server. Then when a user's web browser accesses https for the first time, it will object to the authenticity of the new certificate, thus needing to be reinstalled again, or install the CACert root certificate again. You can't win actually as users will always be chasing their own tail reinstalling certificates, albeit infrequently !
Expiration time of the self signed certificate
One last point to note is that the sme self signed certificate is valid for one year, and it gets automatically renewed by sme server functionality on the anniversary of the installation date of the sme server OS.
So if a user installs your self signed certificate into their browser (ie the one issued by sme), then in a year or less time, they will again receive warning messages when they access your site using https, as your original security certificate has expired. The answer is for them to install the newly created certificate into their web browser again, but by that time they have forgotten what they did a year ago, and go into panic mode again and get scared of the warnings, and end up not accessing your site at all due to fear. The result, another time wasting call to your tech support line.
There is a mechanism (custom-templates) to specify how long your sme certificate will last for, eg you can change the validity to say 5 years (instead of 1 yr), if you feel that security model is acceptable, and that will save users from having to reinstall the sme certificate into their browsers every year eg they will be asked again to install it in 5 years (or less) depending when they first installed it.
Problem with email client
Also if using the self signed certificate, instead of configuring your email client to use say mail.yourdomain.com for sending and receiving mail server names, then change that to servername.yourdomain.com, and that way the email client will not create a warning/error each time you access the mail system on your server ie by clicking the Send/Receive button in the email client ie the certificate name will match the requested server name.
Multiple domains
If you have multiple hosted domains, then you may need to use a certificate that covers all those domains, if you want users to access individual domain name URLs, the CACert How to details that. Otherwise if using the self signed certificate just get users to access https://servername.maindomain.com/webmail irregardless of whether they are using a different domain for their receiving/sending email address. In webmail, change the default senders address for each user to match the domain they are supposed to be using. Note that sme server only has one version of webmail installed and it serves all users of all domains.
Hope all the above makes sense.
Read it again carefully and slowly if it doesn't.
This article is based on information given by mary in this thread in the contribs.org Forums.