looks like this is the later released censored version without that scene. really wish I would have kept the originals that I had, they'd probably be worth some money...

Guys the GOG version is uncensored.
Also...pencil?Where in the game can you get the pencil?
I know there are two ways to solve that puzzle and I've done them but a motherloving pencil?
;p

I played the original Phantasmagoria recently (didn't know it was here... I did a bunch of complicated crap to get it to work!). The rape scene was not as you described. In the original he really does force himself on her somewhat graphically. I remember upon release this game had a lot of controversy, so you must have played a censored version.

Gog's version has both the censored and uncensored versions. You can choose which one you wish to play via the options menu.
And please, let's stop calling it a rape scene, there isn't any rape to speak of.
When he first walks up to her from behind she's pissed, naturally the guy had been acting like a moron, but after a while she's kissing and embrancing him.
From there, there's a consensual sex scene that gets a little rough when the guy weirds out. It wasn't the tender loving make-up sex she was probably expecting, but he didn't raped her.

three things:
I agree that the game is flawed. I'm doing my master's thesis on it, and I don't think it's the greatest game ever. I've done a lot of thinking on it, of course, and it's got a lot of redeeming value even for its flaws. The biggest flaw is that it lacks replayability, but any game whose appeal is primarily in mystery and shock is going to have that problem.
Secondly, those puzzles that seem to be game-ending? They're not. There are ways around. I didn't think so, but then I loaned my copy to my brother, and he played the alternate paths for me.
Thirdly, it's a rape scene. It's a really disturbing scene the more you think about it. It starts as rape and it ends as rape. The fact that it goes through a consensual stage in the middle is what makes it really difficult to deal with, psychologically. It shows Adrienne's internal conflict very well. But the directing in that scene makes it very obvious that when all's said and done, Adrienne feels she's been raped. And the law, at least in the United States where the game is set, says that if the victim says it was rape, it was rape. She refused him and he ignored her refusal. That's rape. It's complicated because it's her husband--which is why she does give in, because she's conflicted. But the end of the scene--her posture, her reaction, all of it--makes it very clear that she has been abused. The scene wouldn't have been as controversial if it hadn't been at least a little complex. It's one of the more brilliant moments of the game, actually.
Of course, if you play the censored version, the hint skull mocks you. Silly hint skull!

I still personally find the way the last chapter of the game was set up makes the game feel uncompletable to some degree. You have little to no time to react in some of those instances.
However as to the one topic... I personally don't like rape scenes and would prefer not to have to see it if at all possible, it's bad enough I know it goes on at all. However the scene itself was handled well, as Valanice pointed out in their above post. I own the uncensored version so yeah I can attest to it being pretty much just like they described. It was certainly a far cry from the tender moment they shared together at the beginning of the game when she wakes from the dream.