I ran into some difficulty registering my retail key from Steam. After contacting Customer Support, I discovered that the key Steam was automatically pasting into the activation box was actually my Preorder key. After some fighting with the Steam app, I figured out that it does not want to let you see your retail key until the game has been installed via Steam. Since I'm happy with the program where it is, I ended up having to find a way around this little "feature."
NOTE: This is *NOT* meant as a way to bypass copy protection - I simply did not want to re-download and re-install a game I already have. And given the difficulties that some other people have been having with Steam, I don't really want it to be managing an MMO for me in any case.
The steps I took are as follows, after loading Steam and switching to the "My Games" tab.
1: Click on the game in the Uninstalled list, and select Install.
2: Click through the prompts until it reaches a point where it says that to activate the game, "your Steam Account must be linked with your Star Trek Online account." This page contains a box that would appear to be meant to set up such a link. It will be greyed out and non-selectable. Hit Cancel
3: The game will begin to queue for downloading. Immediately select the game and pause download. Right click, and select "View CD Key" from the list of options.
4: Copy the CD Retail key to the clipboard. At this point you can abort the download and "Delete local content."
5: Go to the Cryptic Activation page, and paste the key into the correct field.
At that point, my key (finally) registered successfully.