Well, looks like Intelligent Systems' PdP site shut down today... it's just giving me a 404 error when I try to access it. Probably not a good sign.
That site had been on up since 1995 or 1996 and a had even a small community on the bulletin board.
The site being taken down does not inspire confidence to me for the future of the Panel de Pon series. Though there is a small chance they took it down because it looked a bit dated (like I said it started back in 1996, I think), or they are planning a major new Panel de Pon release and making a modern website for that.
However, I think its more likely that they decided to just take it down because nothing is being done with the series. The last Panel de Pon game was release in 2007 (though a stipped down port of that game was released for the DSi in 2009).
Typically since the Super Famicom there has been at least one Panel de Pon game released for a Nintendo console since its Super Famicom debut:
Super Famicom/Super Nintendo: Panel de Pon/Tetris Attack
Game Boy: Yoshi's Panel de Pon/Tetris Attack
Nintendo 64: Pokemon Puzzle League
Game Boy Color: Pokemon Puzzle Challenge
Nintendo GameCube: Nintendo Puzzle Collection
Game Boy Advance: Dr Mario & Panel de Pon
Nintendo DS: Planet Puzzle League/Panel de Pon DS (Puzzle League Express for DSi)
There was no new Panel de Pon game released for the Wii, and so far no new game released for the 3DS (which imo represents the last chance for a retail Panel de Pon game to be released).
I think it would be for the best to wait until E3 to find out what is happening to this series (like I said, if a new game is happening it will most likely be for the 3DS or a downloadable title for Wii U or 3DS like Pushmo and Crashmo). However, I am not optimistic.
Nintendo has let so many of their smaller series (Golden Sun, Starfy, Custom Robo, Panel de Pon, Famicom Wars/Advance Wars) basically die out over the course of this generation.