Everything else - including protected Game saves - would be copied over via PS3's build in Backup / Restore option. However - keep in mind that Sony've introduced additional protection a way back so now after restoring the backup to another hard drive in the same PS3 you'd need to reactivate your PSN content (games & DLSc) by logging into PSN - so unusable if you want to keep your PS3 JB-able - same goes for trophies indeed.
Well - I can't confirm that but somebody here in the forum claimed that they've managed to copy the content of old hard drive to new one using the FTP program without need of (re-)activating the content by I've not tested it myself so can't vouch for that.
I believe that since a few updates back Sony introduced linking of the PSN content not only to PSN ID and concole ID but also to the hard drive's serial number. You can actually find the hard drive serial number in registry - hence the possibility if you'll copy the files "manually" rather then using the Sony's build in utility it might (and I say MIGHT) work