eww,
After looking in depth at my /opt folder, all of the files are relevant to two "sets" of software that I use.
1) One variant of a CISCO VPN Client that I used before I upgraded to SL.
2) Everything I've ever installed with MacPorts including: X11, aquaterm, emacs, ffmpeg, gcc43, gdb, gnuplot, etc.
Therefore, it is very likely that if you do not use MacPorts or that specific CISCO VPN client, you might have an empty (or even non-existent) /opt folder unless something that you have installed uses similar methods. Most Linux/Unix-"ish" software like perl, python, gcc, g++, scp, etc. is installed in /usr instead of /opt, but MacPorts installs in /opt by default. If /opt is truly empty, which you can find out by using:
du -h -d=1
inside the folder via the Terminal. It should return the size summary of:
0B .
it won't hurt anything if you delete it. If you do choose to delete it, you will most likely have to do so as root because the permissions are likely set to 755 for user(root)=rwx, group=r-x, other=r-x.
Good luck