So I've been setting up all my sites as separate domain names, with things like code.domain.com and email.domain.com. Should I migrate these services, or is there a way to use HTTPS on many subdomains?
You can buy a global wildcard certificate that lets you create a domain name for *.domain.com. It costs like $199/year on GoDaddy I think, so you'd have to figure out if you think it would be worth it over getting individual certificates as $12/cert.