I think you can do this, but not the way you're trying to do it.
An SSL certificate is a statement binding a public encryption key to an X.500 structure which includes a CN, or Common Name, element; a signed certificate is one such where the binding is verifiably certified by a third-party certification authority, using the a public key already known to end-users (that stack of Certification Authority (CA) certificates living inside your browser).
When you visit an SSL-secured web site with a browser, the signed CN is made known to the browser. What the browser chooses to do with it is up to the browser. The browsers I'm aware of compare it to the host name requested, and error if it's different (or if that certified binding doesn't stand up to analysis, eg the signing certificate is not known to the browser or the binding is out-of-date, but that's a different issue). There's nothing that in principle stops you from getting a publicly-signed certificate where the CN is an IP address not a FQDN (fully-qualified domain name) [1], but that won't magically make the browser compare the CN with the IP address, instead of with the requested hostname.
I suspect the simplest way to solve your problem is to start your own CA, which is easy to do, and there are many public tutorials about; one is here. Once your end-users import your CA into their browsers, all certificates you mint will be accepted as authoritative.
You may then have a second problem in that you want to run a lot of NameVirtualHost sites on a single IP address. This has historically been insuperable, since (unlike TLS) SSL negotiation happens before anything else on a connection; that is, the CN embedded in your certificate is made known to, and used by, the client before the client is able to say what host they're trying to connect to.
Recently, a protocol extension called SNI (Server Name Indication) seems to have been introduced, which allows client and server to indicate that they'd like to do some host name stuff before the SSL certificate is presented, allowing the right one of a set of certificates to be given by the server. Apparently this requires apache 2.2.10, a sufficiently recent version of OpenSSL, and (importantly) client-side support.
So if I had to do what you're trying to do, I'd be looking at minting my own CA certificate, telling my end-users that they have to use browsers that support SNI and import my CA root certificate, and cutting and signing my own SSL certificates for each bugtrack site.
[1] OK, you may not have found anyone who'll do it, but that's an implementation detail. What I'm trying to show here is that even if you did, it wouldn't solve your problem.
Is it possible that the lines are ^M-terminated? This is a potential issue when moving files from Windows to UNIX systems. One easy way to check is to use vi in "show me the binary" mode, with vi -b /etc/apache2/domain.ssl/domain.ssl.crt/domain.com.crt.
If each line ends with a control-M, like this
-----BEGIN CERTIFICATE-----^M
MIIDITCCAoqgAwIBAgIQL9+89q6RUm0PmqPfQDQ+mjANBgkqhkiG9w0BAQUFADBM^M
MQswCQYDVQQGEwJaQTElMCMGA1UEChMcVGhhd3RlIENvbnN1bHRpbmcgKFB0eSkg^M
THRkLjEWMBQGA1UEAxMNVGhhd3RlIFNHQyBDQTAeFw0wOTEyMTgwMDAwMDBaFw0x^M
you've got a file in Windows line-terminated format, and apache doesn't love those.
Your options include moving the file over again, taking more care; or using the dos2unix command to strip those out; you can also remove them inside vi, if you're careful.
Edit: thanks to @dave_thompson_085, who points out that this answer no longer applies in 2019. That is, Apache/OpenSSL are now tolerant of ^M-terminated lines, so they don't cause problems. That said, other formatting errors, several different examples of which appear in the comments, can still cause problems; check carefully for these if the certificate has been moved across systems.
Best Answer
The contents of that green bar come from the certificate itself, which you will have to get reissued to change it. The certificate's O attribute in the subject (organization), along with the C attribute (country) determine what is displayed. If they are absent, it will simply display the primary subject domain name from the certificate.
Also, the name (and usually the green bar) is only displayed for EV (extended validation) certificates. If you don't have one, you would normally have just the domain name, or no information bar at all. How this is displayed is of course dependent on the browser; recent versions of firefox display your domain name on a teal background in the address bar for non-EV certificates, whereas chrome just displays a lock icon and formats "https://" in green type.
You can't get a wildcard EV certificate, so to get this functionality in most browsers you would have to see if they would issue you an EV certificate with each of your subdomains as alternate names (the one that signs verisign.com is like this).
Verifying your company name and number, and usually inspecting your personal ID, incorporation, and a document giving you authority to act on behalf of the corporation are all expected parts of getting an SSL certificate issued in your company name at all.