File format proliferation is probably a feature in every field. What I know is quantum chemistry, and I'm continually frustrated by the myriad file formats that are out there. The reason I bring this up now is that I recently looked at the Chemical Markup Language (CML) and was quite impressed.
I've been lukewarm on CML in the past. The first CML files I saw had constructions like <floatArray builtin="x3"> followed by a long list of x coordinates, and smacked of dusty deck fortran code. I should have dug a little deeper. Even in those days, there were the ability to enter information in terms of <atom> tags.
What has me so excited now is the ability to use <crystal> tags to input unit cell information. That, coupled with the ability of the excellent Jmol program to display them, gives those of us working with both finite and periodic molecular geometries a single file format that can handle many of our needs.
I should also point out the excellent OpenBabel project, which gives a way of converting between many of the molecular file formats. I should no doubt use it more often than I do.