It is possible to transfer over my "Copy Protected" game saves? If so, do I retain the ability to gain trophies with that save file?

Assuming your old PS3 is still functional, this should do it:
http://www.youtube.com/watch?v=qM4anitZic0

1. Update both systems to 3.15 or up.
2. Hook both systems to your TV.
3. Deactivate the source PS3.
4. Activate the destination PS3.
5. Turn off systems. Link both systems with Ethernet cable.
6. Turn both systems back on.
7. Go to Data Transfer Utility, proceed and select option 1.
8. Switch TV source to destination PS3.
9. Repeat step 7, except choose option 2.
10. Let the destination PS3 format.

Thanks. I just saw that feature on my old PS3.

Everything in my home is running wireless and I threw my remaining ethernet cable out about 2-3 weeks ago.

Now I wish I hadn't.

No problem. I'm not sure if the backup function works in the same way as the transfer function does, but you might be able to do this with an external harddrive instead.

Might have to look into that and see what I can do.

Now what if I were to begin playing some Killzone 3 on the new machine, setup my PSN account, save some games, etc... could I still transfer my other stuff from the old PS3 later on?

Damn, found out that it will just overwrite anything on the new PS3, so no point in starting a game only to lose the progress. 

Time for me to choose...

All of my save files or being able to play it now as opposed to tomorrow or whenever I get an ethernet cable.

Fuck it, i'm just gonna forget the copy protected game saves.

Should still be able to gain trophies on the others though hopefully.