It depends on your background. People like myself will probably continue to use both. Fontographer for drawing and FontLab for the more technical portions.
Fontographer is for people like myself with a long history of drawing with Béziér curves and working in typography. Because FreeHand was developed out of Fontographer, FreeHand experience is good. Illustrator and InDesign experience also translates well. This is a superb drawing program for typographers who want to take the next step.
Fontographer is a wonderful drawing experience. It has been a real joy to experience that fun again. After nearly a decade in FontLab, font design is fun again. There are some limitations. Adding the character slots for Eastern European, Cyrillic, or Hebrew characters would be a real pain, for example, without an existing sample font. Fontographer cannot write OpenType feature files. You cannot show the names of characters in the font window unless they are Unicode glyphs—and characters for oldstyle figures, small caps, small cap figures, denominators, and so on do not have Unicode names. Its hand letterspacing tools are really quite good. Plus, there is the power of its Auto Space and Auto Kern controls. Fontographer does a marvelous job of auto spacing.
FontLab is a professional font design program for people who went to school to learn font design and people working in the font industry. Its interface is not nearly so intuitive as Fontographer, but it is much more powerful. You can control it with Python scripts, you can write OpenType features within it. It can do class-based kerning easily and well. It has a superior interface for people who need to hand produce all the letterspacing and kerning in a font.
It does really well at generating new glyphs for special encodings. It can automatically add any new glyphs used by an OpenType feature set, use multiple master fonts for building font families, work with up to 64,000 characters (for Asian fonts), right-to-left (Arabic and Hebrew) text support, programmable font transformation, encoding templates, editing CMap files, manual TrueType and Type 1 hinting, and test fonts with Font Auditor. Plus it can show character names in the font window.
We need to get this question out of the way before we get started. Personally, I started in Fontographer in the early 1990s and gradually built a little sideline of designing fonts. They were selling a little on Myfonts. When OpenType became viable with the release of InDesign I needed to find something else. My old version of Fontographer would not run in Mac OSX very well. Thomas Phinney, then of Adobe, told me I had no option but to go to FontLab. This transformed my career. I learned how to write OpenType features. I learned how to carefully and professionally hand space fonts. I learned an entirely new way of drawing that was necessitated by FontLab's tools. It was eight years of hard work.
I wrote about what I learned in a book called Practical Font Design. It is the book on the left in the center column. It was and is still surprisingly popular. Earlier this year Ted Harrison, president of FontLab, contacted me to see if I was interested in bundling Practical Font Design with his software and possibly writing a version of Practical Font Design for Fontographer. I was and am grateful for the opportunity. Plus, I was really looking forward to relearning Fontographer, now in version 5.1.
The result was the book on the right side of the center column: Fontographer: Practical Font Design for Graphic Designers.