SquawkBox 2.x had an FMC and a TCAS. Where have those gone?
SquawkBox 3 was a complete rewrite. It was designed to provide core functionality related to getting you connected to online air traffic control networks. An in-cockpit FMC and TCAS are peripheral to this purpose and so were not included. Numerous add-on aircraft feature these gauges and more and more are being made SquawkBox-compatible all the time. See the SquawkBox SDK for information on how to do this. If you are looking for a freeware TCAS gauge, Lee Hetherington has written an excellent one. It also includes a SquawkBox-compatible transponder. You can download it from AVSIM here. For a good freeware FMC, try the one created by P8R Software. For those nostalgic for the SquawkBox 2.x FMC, it can still be used for navigation while you are running SquawkBox 3.