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.
The General group of Alternate 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.
These abilities are the ones that 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.
These abilities are specific to one class (in our case - magicians).
These abilities include some that are only available by completing quests (e.g. the Dragons of Norrath progression quests), Veteran Rewards, and the glyphs.
These abilities are specific to the magician's damage spells from The Darkened Sea (level 101-105).
With the Call of the Forsaken expansion our mercenaries can now earn alternate ability experience and learn their own special mercenary abilities. A mercenary must be unsuspended to gain experience, and they have their own tab in the alternate ability window.
The experience and abilities are the same across all your mercenaries. A few of these abilities are useful to any type of mercenary. Other abilities are only relevant to specific classes of mercenaries, for example Healing Acumen is only relevant to healer mercenaries.
There are a number of Alternate Abilities that are important for a magician to learn. Some will apply whether the magician is soloing, grouping, or raiding. There is no single right order in which to learn these abilities, especially since it will vary based on the play style of the magician, or whether they raid or solo or do both.
To use (activatable) alternate abilities in a macro you can use the command "/alternateadv activate" followed the the appropriate ability code, as listed here. This command can be shortened to "/alt act". For example, "/alt act 441" would activate the Aegis of Kildrukaun assuming it was available. The command "/alt list" will provide a list of all (active and passive) abilities available to your class.