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In an effort to keep this guide shorter, I linked all the JAs & Stratagems to BG wiki since almost all of them have gear that augments them in different ways the guide would take several pages in legnth to list them all here.
Tabula Rasa: 3 minute duration: 1 hour recast.
This is your 1 hour and a good one at that. It lowers mp cost/casting time/recast by 10% for all spells and raises all skills to a B+ level. It rechages your stratagems and gives you infinite stratagem charges. Above all it enables you to cast Embrava and Kaustra.Light Arts: 2 hour duration : 1 minute recast.
It raises your enhancing, enfeebling, healing, and divine skill from its normal D skill to a B+ skill. It reduces mp cost/casting time/recast time by 10% for light magic spells while increasing the same stats of dark magic spells by 20%. Lastly it enables you to use light based stratagems. Whats a stratagem? Stop jumping ahead in the lecture. Overwrites Dark Arts.Dark Arts: 2 hour duration : 1 minute recast.
The reverse of Light Arts. It raises your elemental, enfeebling, and dark skills. Overwrites Light Arts.Modus Veritas: Instant : 3 minute recast.
When used on a monster after a helix spell, the Helix's DoT is doubled while the duration left is halved.Sublimation: charges until it is 25% of your max hp/charged has 2 hour duration : 30 second recast.
Scholar's native way of restoring its own mp. Upon the initial use you slowly lose 2hp/tic to gain some ammount of mp in a "sublimation tank", which upon the second use of the ability is transfered into your mp pool. At level 99 you will gain 8mp per tic which can be further increased with gear.Libra: Instant: 1 minute recast.
Shows your party's enmity ammounts. It is a proc in voidwatch and a JA proc in dynamis.Caper Emissarius: Instant: 1 hour recast.
Transfer enmity to a party member of your choosing. Quite nice when you pull hate to stick all that hate onto a tank.Enlightenment: 1 spell: 5 minute recast.
Your only merit JA. This enables you to cast a spell from either addendum(next section). The light/dark arts penalties will still apply, but this still has uses. Merits after the first increase MND/INT by 5 for the spell you cast.
Stratagems are used by consuming a "charge". At level 99 1 charge is restored every 48 seconds and you can store up to 5 of them. You can use any of these in combination (assuming they are from the same school) but can not use 2 of the same stratagem on a single spell. The effects of the stratagems in either art are almost parallel; each gaining a stratagem with the same affect on its respective art. For these we will use (LA) and (DA).
Penury(LA)/Parsimony(DA)
Halves the original MP cost of your next spell.Addendum: White(LA)/Addendum: Black(DA)
Enables you to cast more spells. More on this in magic. These are the only stratagems that last more than 1 spell. It will stay active until you lose your current arts.Celerity(LA)/Alacrity(DA)
Halves the casting time and recast of your next spell. This stacks with any other form of recast reduction like haste but overwrites the 10% reduction from arts.Accession(LA)/Manifestation(DA)
Makes your next spell Area of Effect by doubling the original mp cost, casting time, and recast. More on which spells this works with in magic.Rapture(LA)
Increases the potency of your next cure spell by 50%. Also increases Banish damage for lulz.Ebullience(DA)
Increases the potency of your next nuke by 20%. Works with nukes/helices/kaustra/drain/aspirPerpetuance(LA)
Doubles the duration of your next buff.Altruism(LA)/Focalization(DA)
A merited stratagem. Increases magic accuracy by 5 for each merit.Tranquility(LA)/Equanimity(DA)
A merited stratagem. Lowers enmity by 10 for each merit.Immanence(DA)
Enables your next spell to be used like a WS to make a skill chain.
Immanence is one of the more difficult stratagems to employ effectively due to the way skill-chains work. What Immanence does is it makes your spell count like a WS w/ 1 property of the specific element. This works with all WS's. So if you commonly play with the same people, it is a fun to set up skill chains with them. Immanence spell>WS>sc(lvl 2 60% dmg)>WS>(SC light/drk 150% dmg) is a very nice way to get a lot of damage out of a very cheap nuke. You also may find that you are basically solo and want to MB off yourself. It takes at least three stratagems to get the full use out of it. Imm > Imm > Ebul. If you want to MB w/ a T5, It will need to be Alacrity'd(stratagem) to reduce the casting time. Although this is only really something I would do for Kaustra, I'm including some you might want.
immanence aero > immanence noctohelix >Gravitation> Kaustra (MB)
immanence blizzard > immanence water4 >Fragmentation> Ionohelix (MB)
immanence fire > immanence Thunder4 >Fusion> Luminohelix (MB)
immanence Luminohelix > imm+ebul+alac stone5 >Distortion>(parc+ebul) Shattersoul >Darkness> Kaustra (MB) got infinite strats anyway, why not?
Enhancing Magic 8/8 is your priority here. MP, MND, INT, Enfeebling, Elemental, Dark, Healing are all good bonuses for whatever your situation calls for.
Group 1:
Grimoire Recast: If you find both arts on cooldown, probably just sit in light arts. keep people alive > deal dmg.
Modus Veritas Duration: would be better if it didn't miss all the time.
Helix Magic Acc./Atk.: Very nice, 5/5 this.
Max Sublimation: Very nice, 5/5 this.
Group 2:
Focalization(DA): Next spell has a bonus to m.acc. Useful for sticking enfeebles like Impact on harder content like Delves & high tier battlefields.
Enlightenment: is nice for getting 500 skill without as much gear.
Stormsurge: Up to +12 stat with gear & 5/5 merits. Highly suggested.
Bolelabunga: A great idle and regen club.
Chatoyant Staff: cure with this when you have light weather.
Tamaxchi: cure with this when you lack light weather.
ToM Staves: Best casting time / recast time down weapons hands down. Put in precast sets if you own and midcast sets where they won't hurt output/accuracy. The inventory loss is pretty hefty for their limited use if you keep multiple. The only one I normally use is the thunder recast for stunning.
Kirin's Pole: Augmented using Genbu's Scraps, it can get +12 enhancing magic skill. Great for hitting 500+ for cap'd a embrava.
Earth Staff or 
Terra's Staff: No major difference between them. They are ideal for your PDT / Turtle sets.
Chtonic Staff: Great MDT staff, but with the pdt+6 it is not ideal for a turtle set.Nuking Staves, ordered from weakest to strongest.
Eminent Staff: Basically free, this is one of basic staves to start with; only bother with one.
Baqil Staff: Another starting staff. Can be augmented with +30 m.acc allowing this to stay useful for a while.
Atinian Staff: AH starting staff, not on the AH often. This will help you until you get something better.
Coeus: Until you get the Bolelabunga for regen potency, this is a good regen staff, as well as the best of the starter staves.
Ngqoqwanb: Ice magic atk bonus ... sounds like the same as VW terminology for Ice Potency +2. The best staff for blizzard spells if magic accuracy is sufficient.
Twebuliij: Path B augment provides a great magic accuracy staff, and it isn't a shabby damage staff either.
Venabulum: A very strong staff, but can be difficult to get. not as much m.acc as Path B: Twebuliij or Lehbrailg+2 with proper augs.
Lehbrailg +2: Augments are random, can beat Venebulum and Twebuliij with proper augments.
Hvergelmir: Empyrean staff. Great dmg & m.acc. no INT / MND which is a bummer though, at least it gets lots of MP.
Tupsimati: Mythic staff. Great dmg, m.acc & reduces enmity gain for spells matching weather, again with the no INT / MND :sadface:. T1 aftermath for even more m.acc or T2 aftermath for more MAB. This is the best of the best for SCH. 
are also nice for the events they are active.Last, you should try to acquire some movement speed gear:
or
can be augmented with movement speed +8%.Defense No TP Loss was made with Tupsimati in mind. Gendewitha+1 has 1~2 more defense per piece and usually more vitality. Also has only 5 possible secondary augments compared with the 11 of hagondes+1. It's possible to get -2PDT from the Black earring but extremely rare so getting two would be extremely time consuming. The set has a possible -15%DT, -36%PDT & -22%MDT. which gets over both the PDT & MDT cap. decent play room with MDT but very little play with PDT.
Cure - potency up to 50%>healing skill>mnd>vit for amount cured. One could worry about enmity and such, but in almost any situation you have 2+ DDs that should hold hate off of you. Chatoyant is better than any other staff if you have 38+% cure potency or more including the 10% on the staff assuming weather is maintained.
If using Rapture: equip
and some other "Cure" Potency pieces to bring it to 50%.Cursna - Gear for Enhances Cursna effect and quick Recast equipment.
Enhancing - An ideal set consists of 500+ skill while wearing af3+2 hands. It helps stuff like enspell/phalanx/barspells and embrava. Kirin's gets an augment of 4-12 w/ a genbu scrap.
Basic set has only relatively easy to obtain equipment, try for at least +30 skill in gear for a total of 450.
Bookworm's Capes obtained from Incursion can have Regen augments.
Enfeebling -Stats: magic acc/enfeebling skill. In addition, use mind for para/slow.
Nuking - Some times you just gotta zap a bitch with lightning bolts ya know? To learn about how magic damage is calculated: Magic Damage.
The following calculator allows for gear/merits/mob and several other variables: here
The following sets will not be the best in all situations, please use the above mentioned calculator to figure that out.
The magic accuracy set is more or less a bunch of pieces to choose from to help get enough magic accuracy so you will not have issues bringing down auras and is in itself over the top.
The list is of non-weapon magic potency gear.
The Obi should of course vary based on what you are casting.
If the day matches the nuke replace a ring with: Zodiac Ring.
Stun - This should be one of the first sets you attempt to finish. Aim for recast reduction and magic acc. You of course want to have a good land rate, but going for that over the top acc to make sure you are capped vs shaving off that extra second or 2 on recast is largely based on the situation.
Impact - That's right. I'm telling you to get a twilight cloak. Impact gives an amazing -20% stat effect that lasts for up to 3 minutes. Use w/ ES on very strong mobs to make them much easier. I also would use Parsimony w/ AF3+2 legs to try to deal w/ the 666mp cost. The rest of the slots can be filled with MaB or macc/elemental skill depending on how hard your target is.
Helix - Helices have a lower base damage than normal nukes AND a low dINT modifier benefitting highly from Magic Damage.
Drain/aspir - The following enhance the potency of drain & aspir spells directly. Aside from them, put dark magic skill anywhere possible to increase the ammount recovered and recast gear everywhere else.
Kaustra - Very good for soloing BCNM/KSNMs as it is a ridiculously strong especially at lower levels.
dINT modifier based on level making it slightly less than a highest tier nuke at any given level, low base damage and not affected by the 'magic damage' stat. Depending on the target, Moepapa > Eddy neck | Ombre > Erlene's Notebook ammo | Strophadic > Novio ear. The rest likely only needs to be swapped out when more magic accuracy is necissary.
Inventory
While we can now use more than 80 slots for gear, it would be prudent to keep the gear use to a minimum so one could still job change within 30 minutes... so much gear.
1: SKILLUPS!! get your enhancing/enfeebling/elemental/dark magic skills cap'd. Also mildly useful to get 300+ staff skill for cataclysm & 1 merit into shattersoul for solo content.
1.5: A full set of sparks gear?! This is your baby set. If you can, get yourself a better staff otherwise this will do fine for your next step.
2: Yorcia / Ra'Kaznar Skirmish: This is going to get your base gear that can be used in multiple situations(pdt/mdt/nuke/refreshidle) until you can obtain/afford optimal sets.
3: Stun practice: go into the wilds with a friend and practice stunning by animation. You will need this skill if you want to be able to progress through delve.
4: Delve: In the first three delves your role will be mostly just to stun, in the others you will likely be doing more nuking or taking the role of the whm.
Update version: 4 September 2014; v0.9