Does anyone else's manual have the ships at the bottom of the page? Because mine doesn't and Moo still seems to ask me to id those ships.

appearently, this isnt so - your save gets disabled...and some report a lot of ships missing as well

Same problem here. After awhile you get the copy protection of identifying the ship, and if you guess wrong you're done.

One thing that should be noted is that SimTex were very sneaky with their copy protection, where if it detects that it's been altered then it messes with the game later on. I can't remember if there was a crack which properly deals with this or not, so be careful!

To my knowledge there was never a 100% working crack for it, you just had to have the manual or risk having your game ruined later on.
I was surprised to read that GOG solved it, but I guess they didn't :p
The inclusion of the "answer sheets" should solve this, but I wouldn't like to be GOG support in a few days.

Viper is not in the reference card (but it appeats in game in recognition window).

The GOG version seems to have cracked it. While the QRC doesn't have any ship ID info (at least not on the one I downloaded from here), the game plays fine after clicking any of those pictures at random. Random clicks worked okay for me on the four times the copy protection came up.
Edit: are any of you actually seeing ship recognition pictures somewhere? The reference card I downloaded is only ~11 pages long and contains no pictures of spacecraft.

Start -> GOG.com -> Master of orion 1 + 2 -> Master of Orion 1 -> docs -> Reference Card

Not sure why I was looking in the wrong place, since it was linked earlier in the thread. I was confusing that file with the one available for download after purchase. D'oh.
Either way, it seems copy protection is cracked for GOG so ship recognition isn't particularly necessary

Is the copy protection really completely cracked? I've had a couple of games now and each time I get to the copy protection, click the top left ship, then within a couple of turns in the game all the other races have declared war against me and relations have gone to hatred (even those with which I had friendly relations and a non aggression pact). It may be a coincidence, but it really feels like the game is purposefully doing it because i got the ship selection wrong.

Any progress on this? Szumo is right, no Viper on the Ship Recognition Card. So if it is showing up in game then maybe we do not have right card?