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!
How do I connect to a server using a GameJolt profile?
In order to ensure that the player is using a GameJolt save, the player needs to log into GameJolt first, then click Play Online. Once the player's profile card appears, click it without holding SHIFT (Holding SHIFT skips the server list screen). If done correctly, then the server should accept entry.