it's been a while since i've used clonecd, and i can't remember how I evaluated it. i know it'll do a bin/cue, and it'll add an extra file for subchannel data, which is unnecessary for sega cd games.
i also haven't used nero to image anything for a while. does it do anything other than it's proprietary format? i think nrg is fine for imaging and backup, but there's unnecessary data in the file, so it's harder to poke around or apply a region patch.
when i was a lot more active with archiving a good copy of every sega cd game (7+ years ago, holy shit!), i did a bunch of testing of all the popular cd imaging/burning apps. i think i ended up liking blindwrite suite 4 the best for reading, and cdrwrin for writing, although writing was less of a concern than having a pristine image. i thought i had notes of all this somewhere, and i wish i could find them because i'd like to know what i thought of clonecd. i also remember trying alchohol 120% at a couple different times during its development and it always fucked up the cue sheet, putting 2 seconds of silence at the start of every audio track.
unfortunately i think blindwrite quit being a viable option when they got to version 5 for some reason. the only point where nrg outperforms other formats is dual session discs (dreamcast games) and that's only because discjuggler was a rediculous piece of shit. discjuggler is a poor choice for sega cd games as well, now that i think about it.
i think i've rambled off most of what i remember. carry on.
