I like the ClearView ($39 shareware - now and for all future upgrades) flight simulator, that works perfectly with the E-sky flight sim USB controller (about $20). ClearView has photo-realistic sceanery, lots of free models to download (including the HBK2 that I could never find for FMS (which does have terrible graphics)), and the ability to do weather and various training modes. I think it could probably do 3D if you had a model definition set up for it, but I have not tried that....

ClearView link: http://rcflightsim.com/download.html

E-sky controller link: http://www.raidentech.com/e4chflsitrki.html

Hope this helps!