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!
I hear this game can be modded, where do I find mods?
You can find threads about all released projects here
The wiki has information on their use, as well as pages for each project here
Content packs are what you want if you are looking for new textures, music, sprites and sounds.
Modifications do what the name implies, they modify the game files. Currently this requires overwriting the base game but in the future it will be easier.