The programs you mention aren't directly comparable.
The Profantasy program that competes with Fractal Mapper is Campaign Cartographer 2 Pro for $39.95. Both Fractal Mapper and CC2Pro are full mapping programs that let you create maps and then add symbols to them. CC2 is more complicated but more powerful, FM is easier to use, but a little less versatile.
Fractal Terrains is a program that creates random, fractal based worlds, which you could then edit and add symbols to with either of CC2 or FM (easier with CC2, being from the same company.).
If you have time to learn the program, and really love mapping, I'd advice CC2Pro. If you just need an occasional map, go with Fractal Mapper. If you are starting a campaign from scratch and want a really cool world map, or are running a sci-fi campaign or other game in which PCs visit multiple worlds, I would additionally recommend FT, which is a stand alone program.
Edit: Dungeon Crafter is a free program that lets you create tile-based dungeons. There are some limitations, but for free, who's complaining? There are other commercial programs for dungeon mapping if that doesn't completely meet your needs (Dungeon Designer 2 is an add-on for CC2Pro, for example.)