Patch 4.0.1 completely changed how the glyphing system works, added new glyphs and also changed around the values and effects of a huge number of existing glyphs. It may look complicated on the surface, but with a bit of time and patience you can easily navigate the new glyphs and figure out what's best for you and your spec.

4.0.1 added a new type of glyph: Prime Glyphs. Primes fill the role that used to be occupied by Major Glyphs, they're the ones that will buff your primary healing, damaging, or tanking abilities and will have the greatest impact on your min/maxing.

Guide to Patch 4.0.1 Glyphing.