Resolution
If you have a really weak system, then set this to minimum.
If you have an LCD, set the resolution a notch below your maximum resolution, e.g. for 1680x1050 native that would be 1600x1024 if your monitor supports it, else resort to 1280x800. If you set a resolution other than your monitor's native one, then it will perform resizing. The result is very similar to using Antialiasing. Of course the image isn't as sharp as using the native resolution, but this is minimal and your graphics card can focus on more important things.
For CRTs this does not apply. Choose a resolution that you consider detailed enough, or even your monitor's native resolution if your computer can handle it.
Aspect Ratio
Cryostasis allows you to set an aspect ratio for all resolutions. This way you can enjoy widescreen gaming even with low-res 4:3 resolutions. No performance impact.
Vsync
Forces your graphics card to wait until your monitor is ready for the next frame. This not just limits the maximum framerate to your monitor's refresh rate, but it also slows down your graphics card due to the artificial delays. Quite an impact on performance for the more or less often appearance of frame tearing. Deactivate it if possible!
Gamma Correction
Usually no need to meddle with this, unless you find the picture to bright or dark. No impact on performance.
Shader Model
The shader model is a specification that defines the complexity of graphical calculations. It has a massive impact on performance, but also on visual quality. In case of Cryostasis, a lower shading model results in differently looking visuals. However, as with all judgement calls, visual improvements lie in the eye of the beholder. I couldn't really say that the SM 2.0 visuals looked worse than the 4.0 ones, even though they looked different. In fact, the difference was rather minor. Playing the game with SM 2.0 gives you a very nice performance boost of up to 100%.
Hardware Physics
If your hardware supports Physx rendering (Nvidia Geforce 8xxx family and up), then activate this to get a massive performance boost of up to 300%
Advanced Physics

Applies Physx rendering to many of the smaller objects. Huge impact on performance with no gain in visual quality!
The physics in the game seem rather unrealistic, e.g. you walk against a barrel and kick it through half the room. Same goes for many other objects, so deactivating this option saves your comp a great deal of work without much change in gameplay, or how often do you plan on bumping into objects? There aren't that many anyway. Basic physics stay activated, so you will still see icicles break realistically and this is what you will see most times in the game anyway.
Texture resolution
Use this setting carefully. Many people only think about the quality they can achieve with it, but don't forget that high res textures also eat up more VRAM. I Suggest setting it only to high if you have at least 896MB of VRAM.
Even if you set it to low, the game will still use high-res textures in some occasions, for example for enemies. So keep that in mind.
Normal maps
This feature's task is to improve shadow quality without raising the polygon count

Specular Maps
Sets the quality of specular rendering. Reflections on shiny textures change realistically according to player's location and point of view. Performance impact can range from minor to big, depending on your hardware's ability to support this feature natively. Considering a nice balance between visual quality and performance, you can turn set this feature to low. Even though the game makes use of multiple light sources per scene, the effect is not visible enough due to the similar looking lighting in many areas.
Shadows
Enables shadows. Setting it to high can drain up to 25% of your framerate compared to not using it at all, depending on the level and your hardware. Using medium halves the performance drain.
The loss of shadows is manageable in my opinion. The game uses static shadowing for textures, so you will still see shadows on the walls. You'll just lacking dynamic shadows, so deactivate this feature if you need a mighty performance boost for a reasonable trade in visual quality.
Motion Blur
Self-explanatory. Didn't realize any impact on performance with it enabled.
Camera Motion Blur
Same as above.
Water Reflections
A very nice looking, but subtle effect. Disabling it is good for a 15% increase in performance in water-heavy areas. Due to the subtlety of this effect, I suggest deactivating it if you struggle with your framerate. Turning it off will not disable light reflections on the water, but only reflections of the ceiling.
Water Caustics
Calculates spots of light on objects near water by calculating the reflective abilities of water. Might cause up to 25% of performance loss in water-heavy areas with complex lighting. Deactivating it does not mean that you can't see reflections of light sources in the water any more, but only that the reflection of these reflections on other objects are not calculated any more.
Anisotropic Filt.
Applies filters to textures to further improve their quality. The effect is hardly visible. In fact, I could only see a difference by taking screenshots and comparing them to each other. Strangely enough, at low resolutions the effect seems to be the strongest while having no real impact on performance, while performance went down a good 10% on high resolutions without any noticable difference. Results on your hardware might vary.
Make sure to check out whether you can see a difference with this option. If not, then turn it off. It eats VRAM like a fat lady eats candy and might very well be a reason for crashes if you run out of RAM.
Antialiasing
Smooths out jaggies. This option is tricky. On my system I only recognized a 5% impact on performance, but the result might vary greatly for other setups.
Keep the following in mind: Antialiasing gets rid of jaggies by going mainly through two procedures, raising the pixel count for edges and blurring them. Especially the latter can be seen very clearly in Cryostasis. You can have that for free by using the resizing algorithms of your LCD-screen. Also, the pixel count is usually sufficient on high resolutions. On 1680x1050 the jaggies are so fine that they are not noticable unless you're looking for them. Even turning on AA doesn't have any effect on them any more. Consider this when using this option. I've seen people complaining about not being able to play this game at 1920x1200 with max AA. The idea itself is asinine, as a higher pixel count doesn't do anything than put extra stress on the graphics card without any noticable change in smoothness. Also, don't forget that AA means smoothing by blurring. Apart from the fact that your picture loses sharpness along the edges, Cryostasis already uses motion blurring, which also covers up the aliasing effect.
People who can only run the game in low resolutions will profit noticably from antialiasing. Those, who can run the game in high resolutions should rather turn it off for the sake of quality, or rather use the LCD-trick. Check out my above screenies. The min shots had no AA applied, while the others had it activated. Can you see a difference?