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.
Types of Glyphs
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. They're also boring. Most Prime Glyph choices are no-brainers just as Major Glyphs tended to be pre-4.0.1. As a result, there's less to talk about with this new type of glyph than with the more exciting and dynamic re-done Major Glyphs.
The new UI looks good and is easy to use, what more can you ask for?
Major Glyphs are now the in-between glyph that don't offer linear benefits like Prime Glyphs do, but add utility and flavor to the class. These glyphs often add interesting new mechanics to existing abilities, and Blizzard has used them to give players a lot of the abilities and effects that have been on their wish lists for years. For instance: Glyph of Entangling Roots makes the Druid Root instant cast but gives it a 5 second cooldown and Glyph of Blind for Rogues removes any damage-over-time effects from the target of the Rogue's Blind. These are minor quality of life adjustments but give a real sense of choice and flexibility to the Major Glyphs that is very appealing. You're not going to feel forced to pick up any of your Major Glyphs for min/maxing purposes, it'll mostly be based on your personal preferences and which ones appeal to you personally.
Minor Glyphs are pretty much the same, a couple new ones have been added but they're relatively insignificant and nothing to get excited about.
Ever realize you need to re-glyph and can't find the glyph you need on the Auction House? Or worse, you find the glyph only to see that it's priced at over 50 times what it costs to make? That's all over now. The new glyphing UI allows you to learn glyphs permanently and interchange them at will once you've learned them. All you need to change between glyphs you've already learn is an inexpensive reagent called "Vanishing Powder" that can be purchased from the Inscription vendors.
Say goodbye to sky high costs for re-glyphing.
The UI has been somewhat altered to accommodate the addition of Prime Glyphs, but remains similar looking. It also includes a nice tool which allows you to search for glyphs and filter the results to show both glyphs you already know and ones that you don't. Getting a full set of glyphs is inexpensive and quick if you know a scribe, but if you're looking on the Auction House then prepare to pay through the nose.
Glyph ChangesNearly every glyph was changed in some way, shape or form. Most of the glyphs that were previously Major Glyphs are now Prime Glyphs or have been removed from the game altogether. I'd love to be able to tell everyone what the best glyphs are and what they should be using, but the simple fact of the new system is that there really is no obviously optimal setup for most specs and classes. The best tactic for adapting to the new changes is to get used to the UI so that you can easily search through the glyphs available to your class and decide for yourself which ones to use.
Learning and Exchanging Glyphs
Sometimes the best way to explain something is to show it. Here's a clip of my Restoration Druid's misguided quest to learn and 'equip' the Glyph of Feral Charge:
As you can see, it's easy to sort the available glyphs based on which ones you've learned and which you haven't. You can also look at both together. This will let you see what they all do, and more importantly learn their names so you won't have trouble buying them in Trade Chat or on the Auction House.
Once you've bought the glyph, just right click it to learn it forever. At that point you can select the glyph from the list and choose which slot you're going to put it in. If you've got a Vanishing Powder to consume then a click later you'll be finished. Now log on and get going!