GEDCOM has long been the de facto standard for exchanging genealogical data between genealogy software programs. When you want to share your work with someone else, for example, you export a GEDCOM from your software that they'll be able to important into their software. In theory, as long as both programs are compliant with the GEDCOM standards, nothing will be lost. In reality, not all programs offer 100% support for the GEDCOM standard, so chances are that something will be lost whenever you do this.
FTM supports most of the parts of the GEDCOM 5.5 standard that was released in 1995. The lastest GEDCOM standards are 5.5.1, and FTM, as far as I know, doesn't support those few enhancements. In my opinion, the *minimum* a genealogy program should do is support the GEDCOM standard.
The GEDCOM standard is rather old at this point, and it appears that it will be replaced by something different in the future. Who's to say what that will be? For now, if you want your data to remain portable--either for exchange with others or because you wish to change software--GEDCOM support still remains the de fact standard.
Try googling GEDCOM for more information or check on Wikipedia for more details.