I also share a legal morality with jimbopalmer but can offer some help. I have found myself in a similiar situation - - My ex-wife got the house and the dog but I successfully retained all my software. (I never liked the dog).
To first deal with any legal issues: any violation of copyright would have occurred when the software was installed or whenever it is run from your computer (if it is not yours). Backing this up will not add to any breach of the law. If you say it's yours, despite losing possession of the orginal CD, I'll go along.
1) While the program is running, write down the serial number by choosing About...(your program) from the apple menu. You may be prompted for this number at another time.
2) Copy the progams folder to the archive drive or new mac.
3) Copy your system folder to the archive drive or a differently named folder on the new mac (macs don't like 2 'system' folders). You will only need a few files from the system folder to support your application but if you are moving to a new mac, it is a good idea to have this entire system folder backed up. When you try to start your program on the new mac, you may receive and error that an extension or two are missing. Simply copy the needed extension(s) from your old mac system folder to the new system folder.