We, the pokemon3d.net staff, has from now (2016-09-02) discontinued work on this project and handed it over to a group of volunteers on Github. The project will be open source, and you can help develop it from now on. Check out the repo here.
"Why?" you might ask. We have unfortunatly lost interest in continuing development on Pokémon 3D. Also Nintento of America Inc. sent a DMCA takedown notice to Gamejolt (where this game was hosted) and asked them to remove all games related to Nintendo's work. Read the full DMCA here.
But you can still download the latest version of the game here!
Can I play this game on a Mac or Linux?
As of right now this game is only available for Windows. You might be able to run it thru Wine for Linux. And on your Mac you could run it on a Virtual Machine.
I recommend VMWare Fusion do emulate a Windows installation on your Mac. But you could also use Parallels Desktop or BootCamp.
Community Support thread here: http://pokemon3d.net/threads/1315/