I have a BAT file that unregisters and uninstalls services that I use to do this. But this means that I need to do this on the target machine. I did some digging and came across PSExec from SysInternals. This file will let you execute commands on a remote machine. After some tweaking, I came up with the following command that I am now using in FB to take care of remote COM registration tasks.
psexec \\%TARGET_SERVER% -u Administrator -p MyAdminPassword -w c:\Servers cmd /c unreg_servers.bat
This works very well, and it's one more thing that I now have under the control of FinalBuilder. I also use SysInternal's PSService utility to remotely control the services.
Disclaimer The opinions expressed herein are my own personal opinions and do not represent my employer's view in any way.