By the GURPS RAW, you multiply the energy cost of an enchantment by a percentage based on the coverage of the armor. A full suit (or a shield) is 100% cost, while the torso and groin is 60%, gloves are 5%, and so on.
Since prices are on a sliding scale (from $1/point up to $20-25/point), this really makes breaking up armor as small as you can a big deal. Enchanting individual pieces is generally better than enchanting a full suit. What's more, while getting a larger piece with a strong enchantment can be really expensive, it's not difficult to enchant smaller pieces such as gloves and helmets with a very powerful Deflect or Fortify or Lighten enchantment. A +3 Fortify on a corselet can break the bank in DF (it's 800 energy x 60% = 480 energy, x $20 = $9600) it's cheap on a helm (800 x 10% = 80 x $1 = $80).
Personally, I dislike this in a Guild-centric world. Why pass on your savings? Price-fix it so that you multiply the final cost of the enchantment by the percentage of the body covered by the armor.
At the same time I like the massive price break on very low-powered enchantments. So I house ruled it "final cost" - and now that Fortify costs $9600 on the corselet and $1600 on the helm.
I like the idea that it doesn't reward extra work on your PC - it's a price lookup, not a "how do I just miss the breakpoint?" game.
The tough bit was getting GCA to do this. I could easily do it by hand, but we keep a lot of PCs in GCA partly to do stuff like run the math on encumbrance totals and equipment replacement costs.
Thanks largely to Eric B. Smith, I was able to get this done. The code is embedded here:
Armor Enchantment Cost House Rule Code
Just put that in a text file, save it as "Peters House Rule.gdf" or something and it should work. If it doesn't, or gives odd results, let me know so I can fix my copy!