Once a magician has reached the level of 51 they are able to start learning some Alternate Abilities (AA). Some of these abilities increase the offensive or defensive capabilities of the magician or their pet. A few are alternative versions of the magician's spells (e.g. the Gate ability). There are also some special abilities that are the result of completing progression quests or rewards (such as the veteran abilities for being a long time EQ subscriber).
The abilities are either passive and are always in effect, or they must be activated and will be in effect only for a set duration. There are a small number of expendable Glyphs that are activated and provide an effect for a fixed period of time and then expire.
The first few hundred AA points are relatively easier to get than later ones (this was done to make it easier for newer players to catch up to the veteran players). Most abilities require a minimum level and some have pre-requisite abilities you must know.
Finally, there are a few abilities that are so useful and necessary for a magician (or other classes as well) that many guilds have specific requirements for their raiding members. A good example of this is the Pet Discipline ability that gives the /pet hold command.
There a very large number of abilities, and some are more useful than others, and some not really useful at all. The abilities most often considered "essential" are the ones that improve pet damage and damage mitigation, and the ones that increase the magician's damage. There are also some useful utility spells.
General Abilities are ones that are available to all classes. They mostly deal with a character's basic statistics (e.g., HP, MANA, Strength, resistances), tradeskills, and other things that are available to all classes.
Archetype Abilities are common for a group of related classes. For the magician these are shared by the enchanter, necromancer and wizard classes - the intelligence-based, pure caster classes.
Class Abilities are specific to one class (in our case - magicians).
Special Abilities include those that are only available by completing quests, Veteran Rewards, and Glyphs.
Focus abilities are specific to the magician's damage spells.
Mercenary Abilities are specific to our mercenaries, which can now earn alternate ability experience and learn their own special abilities.