Hi,
a bit late, I nkow, but you should be able to use the "black bar" mode quite easy (at least with an nvidia card)
- open the nvidia panel and go to "flat screen scaling" (or so, I've got the German version)
- select "no scaling"
that should run the game 1:1 with no scaling and black "space" around the (tiny) 640x460 window
nGFX

I would like to know too if there's a way to somehow force Myst to run windowed.
Adding -w suffix to shortcut doesn't work, as the game goes to its normal mode anyway after the window appears on the screen for a second.
There appears to be some fan projects going on to have Myst support, which might enable windowed modes or other options, like ScummVM (http://www.scummvm.org/) and Fissure (http://fissure.sourceforge.net/), but none of these is finished or even in a release candidate/beta state.
Installing a virtual machine of some kind and running game there might be possible, but I don't want to do that.
So does anyone know of a way to have Myst running windowed with (more or less) normal ways, like a small 3rd party application or some window setting?