I'm looking to get an SSL certificate, but I'm not sure just how flexible (or inflexible) they are. Is it possible to have a single certificate that allows:

1) https://www.mydomain.com
2) https://www.mydomain.com:2087 (secure cpanel and whm access through cert)
3) https://www.mydomain.com/~username (allowing clients to take advantage of the certificate)

Is all this possible? If so what are the steps to getting all of the above working with one cert? Also, are the ev1 GeoTrust certificates fine? Anyone have good/bad experiences with them?

hmmm, thats a good question, but I would believe you can, since it's still the same exact domain name, even if it's going through different ports.

I'm sure the cPanel forums has some info on this.

SSL certs should work for the subdomain/domain name. In other words a cert for http://www.mydomain.com will not be good for http://mydomain.com, but a cert for http://www.mydomain.com will work with http://www.mydomain.com/subdirectory.

Sounds good so far. Is there anything I need to do to make WHM and CPanel https work with the cert?

Well, besides installing it i believe you can force SSL logins, there's a guide on webhostgear.com i think.

You may want to create a selfsigned certificate and install it on a unused domain (a domain that doesn't have much traffic and that you don't depend on) and try the process out. I can't remember the specific process, but if you do a google search on open SSL, I believe their main site has instructions.