You could export your scenes to specialist 3D modelling/viewing software. This is what I usually do because the 3D viewers of most GISs are a bit limited (EDIT: in fact I'd forgotten ERDAS Imagine does stereo too but I haven't used it for ages so I can't remember if it is just anaglyph).
EXPANDED (as per Chad's request):
You need to implement a modelling pipeline. This can be more or less complicated depending on your needs and available software. A VERY simple (simplistic?) approach is to convert your terrain to a common modelling format. GRASS, ArcGIS, ERDAS Imagine and GDAL (I think) all export to VRML/X3D. Landserf will export to Terragen. For ArcGIS you need the 3D Analyst plugin. You can then add other elements (e.g. trees) by populating a polygon with points (in ArcGIS you can use Hawth's Tools, ERDAS has a tool in-built, I think GRASS has something similar and you should be able to code something in GDAL/OGR). Convert the points to 3D (interpolate off the DTM) and then instantiate your tree model at each point. Buildings can be done in a similar way (but watch the orientation) if you have a house model or extrude up from your building footprint polygons. The VRML export should honour your textures (it does in ArcGIS at least).
I have also created a pipeline by coding a conversion from GIS data to my 3D modelling package's proprietary model format by using the modelling package's API to call GDAL/OGR, but this is the less simple way.
Alternatively use something like World Construction Set to build your 3D landscape without the need to program your own pipeline or do the slightly nasty VRML export dance.
Once you have your model you could use any package that can show it in 3D (possibly with a further conversion if required). There are loads of viewers/modellers etc. available; some free some not. Have a look here for option: http://www.stereo3d.com/applications.htm
A lot of 3D packages have 3d support now check out Blender, Maya and 3DS Max (?). In any 3D package (including VRML) if you want stereo, you can create two cameras next two each other which can effectively give you stereo if you have active stereo kit attached to your machine.
...and while you're in your 3D modelling package, take the opportunity to improve the texturing and lighting of your model. In my experience the 3D GIS extentsions do this crudely (except for WCS)!