Well until a couple of days ago I did all my PS2 backing up with RecordNow Max 4.5 using Global Images. But when that failed to backup GTA San Andreas, maccarulez1 suggested I try DVD Decryter which you can get completely free of charge from
http://www.dvddecrypter.com.
It's a really small file download too, and it works perfectly.
Just put your original in your DVD drive, under "Mode" do an ISO Read which will write an ISO of your disc to the HDD, then put a DVD-R into your DVD Writer and under "Mode" do an ISO Write.
(There's a point; are you using DVD-R or DVD+R? You should use DVD-R).
Put your finished backup into your PS2 and enjoy.