I know some formats supported replicating copy protection such as SafeDisc to some extent but in most cases you still need to rely on their drivers (Alcohol 120% or DAEMON Tools) to actually work.
There are many proprietary formats for CDs... I'm not sure if your physical media has any copy protection. If not, it's better to stay with standard ones, such as ISO (single track), or BIN/CUE (multi-track).
PS: Alcohol 120% now provides a free edition for both retro and modern systems supporting up to 2 virtual drives, but that edition offers no copy protection support.
UPDATE: Read this before you consider using the free edition. TL;DR: The free edition is not clean.