X-Files guru Frank Spotnitz confirmed on his blog that indeed, a second installment of the franchise is in the works.

Spotnitz said, "A script is indeed in development, but I'm afraid that's all I can say." 

The X-Files ran for an unprecedented length for a genre show, only recently surpassed by Stargate: SG1.  It was known for the moody settings, the crazy mix of urban legends and over-reaching government conspiracies, and the sexual tension between Agents Mulder and Scully.  (Or between Agent Mulder and Krycek, or Mulder and A.D. Skinner, or ... )  The first film came out in 1996, and performed adequately in theatres but never hit big box office success, so a new film's chances are iffy.  Still, the fanbase is still around and possibly interested in new material.