Act 3 on PCE is just an hour or so of cinema after walking through a few rooms. In the Sega CD version, they added a couple of fights/shooting scenes, where you finally fight some Snatchers for real.
A lot of graphics in the Sega CD version have been redrawn or touched up. In my personal opinion, most of the redrawn art doesn't look as nice and most of it was used for the Saturn & PSX versions.
I love both versions because they're both good games for what they are(I don't play too many digital comics). But I really prefer the PCE version and yes, I am biased.
I played the PCE game for years before the Sega CD version. The Sega CD is a nice tech demo for the Sega CD since they managed to get it display almost as many colors on screen as the PCE version.
But to me, its like playing a PS2 version of a game, with a few slight graphical flaws, in regular res compared to playing the Xbox version of the same game in 480p.
The PCE version just looks cleaner and more vibrant. Same with the sound. I love the PSG music and the Sega CD music is still good but sounds too wavy for me. But its very Genesis sounding and the PCE music sounds very PCE, so if you're a fan of either's "chip" generated music you'll be happy.
There are little things too, like the voice effect at the targeting range. The human heads have a cool over the top howl when shot in the PCE game. In the Sega CD game you get one of the Turbo CD Valis III actors sayoing "OUCH!". And from what I remember the blaster effect sounds better and cleaner in the PCE version.
Now, I've been a hardcore fan of cartoons and animation my whole life. When I was younger, I'd scour over TV channels looking for anything animated. After highschool I took a full "classicical" animation course and am qualified to do proffessional animation work(and have done some minor work).
I don't come down too hard on voice acting in games, especially when they're smaller budget. And I can really appreciate the cheezy middle ground between quality, properly directed acting and lowsy poor acting(like the awesome Fist Of The North Star). I think Space Adventure Cobra has some of the best writing and acting around.
But I really disliked the acting in the Sega CD version for the most part. I know everyone(game mag writers) seems to love it and I know that I'm going to get flamed for saying anything so sacreligious, like suggesting that Working Designs was infallible in anyway.
Now, the acting itself isn't all that bad. But we do get some Valis II Magus performances. The worst part for me was the actual voices. In the PCE version, Gillian has the most masculine voice you'll ever hear aside from MAOU GARP in Fuun Kabuki Den. And as if a polar opposite, Gillian in the Sega CD version has the most nerdy-geeky-cheezy-Rogless-from Valis III + Haizen The Ruthless from Valis II voice.
And what really kills me, is I clearly remember(what I said) on the day I was talking to a friend before the Sega CD version was released. We had just played some kind of game, I believe that it was an arcade and by Konami, but it had awful white-washed 1950's Leave It To Beaver style sitcom acting. And I said to my friend, "I hope to god they don't do that to the Sega CD version of Snatcher, imagine if they gave Gillian a voice like that?".
And when it finally came out I was so shocked that they so perfectly captured that awful wimp-wuss voice. And although I don't expect them to get one of the few decent high-pitched english voice actress' to voice "Metal", a queer old man voice is unacceptible. They should've just given it a different personallity or something.
The last part I was dissapointed with was some of the dialogue. However, a lot of the acting and dialogue is acceptible and overall its really just a mixed bag.
But some scenes were so misguidely done, that it winds up being hilarious(just like Fist Of The North Star). When Gillian "accidently" opens the shower door on the wet-naked 13 year old girl, instead of being shocked and embarressed like the PCE version, instead he screams "Woah-ho-huh-hoo!!!!!", straight out of a Porky's movie.
The crap voice trade-off is worth it just for awful scenes like that.
Otherwise, most people have already heard about the scene involving a PC Engine + CD ROM being replaced by a Sega CD combo(I won't ruin the game for you with spoilers, other than getting to see little girls in the shower).
The other noticible difference in a cinema is when 'something' happens and Gillian ends up running behind Random Hagile's bike with his tie caught in it and the other version has Gillian hanging onto the back end of the bike. I don't remember which belongs to which version, but the tie gag was too comical for me(I think that its in the PCE version).
And lastly, I almost forgot to mention that the Sega CD version is compatible with Konami's Lethal Enforcers light gun(I bought it just to get the gun for Snatcher) and is utterly useless.