Here are the Pointer 2 Effects...
Pointer 2 Effects
1 - Nothing
2 - Makes it so the sprite/sequence doesn't look so blocky and square. - Used by Lots of things.
3 - Used by Exit
4 - Used by Meteo
5 - Used by Comet (Looks pretty good using Shell/Protect/Blink graphics.
6 - Absorption-esque effect. - Used by Psych, Drain, Absorb, etc.
7 - Screen Shake
8 - (Seemed to be a multi-Effect, need to test with other Sprites - Targets Allies only)
9 - (Seemed to be another multi-effect, need to test with other sprites)
10 -(Sprite appears first on caster, caster reacts, then vanishes, then sprite appears on targetted enemy.) unsummons - Used by Imp
12 - Possibly keeps the grey palette on enemies when they are petrified and removes the Summon Image. - Used by Roc
13 - Removes Summon Image if applicable - Used by Mage
14 - Looks like a flurry of punches hits Enemy 1, if an ally is targeted, otherwise if an enemy is targeted it will target properl, removes Summon Image. - Used by Chocobo
15 - Shiva's Ice Storm, Moves Shiva's Sprite, Unsummons.
16 - Moves Indra's Sprite, unsummons. - Used by Indra
17 - Jinn flying across the screen, unsummons - Used by Stone, Petrify, Jinn
18 - Another Screen Shaker, unsummons - Used by Titan
19 - Likely used by Mist Dragon, but corresponds to chosen sprites. expels sprite at enemies (looks Really great with Life Sprite chosen) unsummons - Used by Mist Dragon
20 - Seems to be Sylph's healing effect (Figure eighting sprites as they heal) unsummons - Used by Sylph
21 - Odin's Zantetsuken, unsummons - Used by Odin
22 - Leviathan's Wave , unsummons- Used by Leviathan
23 - Unsummons - Used by Asura 1.
24 - Unsummons - Used by Asura 2.
25 - Unsummons - Used by Asura 3.
26 - Megaflare, Unsummons - Used by Bahamut.
27 - Nothing
28 - Nothing
29 - Shows the Sprite/Sequence and Sound Effect Twice. - Used by Explode
30 - Very strange... The effect shows four castings of the spells around the party and the enemies vanish one by one. Only to reappear when the effect concludes, but with a "defeated" sound effect. Oh... - Used by Reaction.
31 - Nothing
32 - Warp's or Dimension 9's revolving aura. - Used by Warp, Demolish
33 - Nuke's (Flare's) Effect. Casted Jinn's effect?
34 - Wave attacking the party. - Used by Big Wave, Wave
35 - Fire 3's Effect.
36 - Nothing
37 - White (Holy's) Effect - Used by Holy.
38 - Odin Rushing Forward - Odin (Enemy Spell)
39 - Sprite/Sequence happens, then screen flashes many different sorts of color - Used by Big Bang
40 - ??? - Used by Fission
41 - Cure 4's Effect.
42 - Screen Flashes Light Blue and then Sprite/Sequence - Used by Glance
43 - Screen Flashes Red, then Sprite/Sequence - Used by Crush
44 - Screen Flashes Yellow, then Sprite/Sequence
45 - Screen Flashes White, no Sprite/Sequence occurs - Used by Gaze, Slap
46 - Sprite/Sequence appears on Caster, then target
47 - Screen Flashes White several times, no Sprite/Sequence occurs - Used by Black Hole
48 - A glitched graphic appears for only less then a second, no Sprite/Sequence occurs
49 - Crashes Game.
50 - The battle screen darkens and does not lighten again, no Sprite/Sequence Occurs.
51 - The Caster Literally jumped across the screen, and then the game crashed.
52 - Screen blacked out.
53 - Crashes Game.
54 - Crashes Game.
55 - No Sprite/Sequence occurs.
56 - Screen blacked out.
57 - Crashes Game
58 - No Sprite/Sequence occurs.
59 - Game goes crazy, then blacks out.
60 - Game Crashes
Here's an ancient post of mine which shows what all Spells Pointer 2 uses.
Weapon Sprites:
Sprite 008 - Thrown Handaxe
Sprite 012 - Thrown Ninjastars
Sprite 014 - Thrown Boomerang
Sprite 016 - Thrown Chakram
Sprite 017 - Thrown Items (Yellow)
Sprite 018 - Thrown Items (Blue)
Sprite 020 - ? (looks to just be glitch graphics)
Sprite 024 - Bow?
Sprite 025 -
I have to wonder if the term "sprite" is a misnomer. Considering that something that couldn't possibly share the same sprite like Peep, Fatal, Float, Quake, etc are listed under the same.
Sprites : 00 Cure1/2/3/4/etc (All to do with Pointer 1 and 2?)
Sprites : 01 Protect/Shell/Blink/Ice1/2/3/Shiva (Summon)/Image
Sprites : 02 Life1/Life2/Asura (RaiseAll)
Sprites : 03 (Looks akin to a Cure graphic)
Sprites : 04 Megaflare/White/Warp/Sleep/Drain/Psych/Nuke/Jinn (Summon)/Flare/Smoke/Sylph (Attack),Bahamut (Attack)/Powder/Disrupt/DullSong/Gas/Demolish/Disrupt(2)/Absorb/Vampire/Digest/Pollen/Fission/MegaNuke/
Sprites : 05 (Same as 03?)
Sprites : 06 Peep/Fatal/Count/Search
Sprites : 07 (Looks to basically be Death Faces from Fatal)
Sprites : 08 Mute/Dispel/Size/Toad/Piggy/Venom/Lit1/2/3/Indra (Summon)/Blitz/Indra (Attack)/Breath/Whisper/Poison/Magnet/Blitz(Enemy)/Thunder
Sprites : 09 (Possibly some explosion graphic?)
Sprites : 10 Stone/Flame/Roc (Attack)/Beak/Petrify/Hug
Sprites : 11 Meteo/W.Meteo/Fire1/2/3/Bomb (Summon)/Chocobo (Summon)/Bomb(Attack)/Jinn(Attack)/Explode/Reaction/Fire/Blaze/Explode(2)/Emission
Sprites : 12 (A breath attack, possibly?)
Sprites : 13 Float/Quake (O...kay?)/Titan (Attack)/Quake(Enemy)
Sprites : 14 Comet
Sprites : 15 Weak/Weak(Enemy)/Storm/Tornado/Glare
Sprites : 16 Hold/Charm/Virus/Mage/Bluster/Entangle/Hold Gas/
Sprites : 17 Fast/Berserk/Wall/Stop (Seems that it's mostly in the pointer 1 for this one)
Sprites : 18 Slow/Heal/Silver Staff/Unicorn Horn/Maser/Heal(Enemy)/Heal (Enemy2)/Beam/Laser/Heat Ray
Sprites : 19 (An explosion of some sort)
Sprites : 20 Hatch
Sprites : 21 Pin/Big Bang/Globe199/Needle/Counter/
Pointer 1: 03 Wall
Pointer 1: 28 Fatal (The rising of the reaper and the energy being taken away animation)
Pointer 1: 37 Quake (To be exact the animation of the chasm)
Pointer 1: 47 Flame
Pointer 1: 48 Flood
Pointer 1: 49 Smoke
Pointer 1: 50 Pin
Pointer 1: 60 Blitz
Pointer 1: 61 Mist (Dragon) (Attack)
Pointer 2: 00 Null
Pointer 2: 01 (The graphic starts from the middle right of the target and descends down slightly before vanishing.)
Pointer 2: 02 Venom/Sleep/Flare/Smoke/Powder/Tongue/DullSong/Gas/Digest/Pollen
Pointer 2: 03 Exit (When you're not actually leaving battle with this, the game gets fairly screwy)
Pointer 2: 04 Meteo/W.Meteo
Pointer 2: 05 Comet
Pointer 2: 06 Drain/Osmose/Absorb/Vampire
Pointer 2: 07 Quake (Shaking of the screen)
Pointer 2: 08 (Looks like a burst of graphic raising upwards coming from the bottom of the screen only ever hitting the party)
Pointer 2: 09 (Graphics assault the enemies and only the enemies)
Pointer 2: 10 Imp (Striking Graphic, over rides defaults Sound choice)
Pointer 2: 11 Bomb
Pointer 2: 12 Roc
Pointer 2: 13 Mage
Pointer 2: 14 Chocobo
Pointer 2: 15 Shiva
Pointer 2: 16 Indra
Pointer 2: 17 Stone/?Jinn?/Ray/Beak/Petrify/Hug/
Pointer 2: 18 Titan
Pointer 2: 19 Mist
Pointer 2: 20 Sylph
Pointer 2: 21 Odin
Pointer 2: 22 Leviatan (Curiously enough there is no sprite or pointer 1 provided for it)
Pointer 2: 23 Asura Cure 3
Pointer 2: 24 Asura Cure 4
Pointer 2: 25 Asura Raise All
Pointer 2: 26 Bahamut
Pointer 2: 27 (Graphic flickers on the target briefly, can be multi targeted)
Pointer 2: 28 (Same as above?)
Pointer 2: 29 Explode
Pointer 2: 30 Reaction
Pointer 2: 31 (Seemed identical to Fission)
Pointer 2: 32 Warp/Demolish/Disrupt
Pointer 2: 33 Nuke/?Jinn?
Pointer 2: 34 Big Wave/Wave (The big difference between this and Leviatan's summon attack is this goes towards the party, though it has pointer 1 as well included in the ability, which doesn't appear to do anything.
Pointer 2: 35 Fire 3
Pointer 2: 36 No graphic even shows, damage just appears.
Pointer 2: 37 White
Pointer 2: 38 Odin (Zantetsuken against party, graphics will glitch if it is not Odin using it)
Pointer 2: 39 Big Bang
Pointer 2: 40 Fission (When used as an ally, the damage effect is shown on the caster and they do the pain animation, does not hurt them though)
Pointer 2: 41 Cure 4
Pointer 2: 42 Glance
Pointer 2: 43 Crush
Pointer 2: 44 (Screen flashes briefly and then it repeats Pointer 2: 27 seemingly)
Pointer 2: 45 Gaze
Pointer 2: 46 Bomb (Summon)
Pointer 2: 47 Blk. Hole
Pointer 2: 48 (No graphic)
Pointer 2: 49 (Crashes emulator)
And now Sequences...
00 - Exit/Drain/Psych/Shiva/Chocobo/Imp/Odin/Leviathan/Blk.Hole/Absorb/Vampire/(Enemy)Odin(Pointer 2 does the work in those cases, or has no graphic, those that have no graphic will be omitted)
01 - Nothing?
02 - Nothing?
03 - Wall
04 - Flare
05 - Fire 1/Emission
06 - Fire 2
07 - Fire 3
08 - Lit 1
09 - Lit 2 /(Enemy)Thunder
10 - Lit 3/(Enemy)Blitz
11 - Ice 1
12 - Ice 2
13 - Ice 3
14 - Armor/Shell/Image
15 - Blink
16 - Fast
17 - Dispel
18 - Mute
19 - Berserk
20 - Stop
21 - Slow
22 - Cure 1/Warp/(Hidden Spell)Disrupt-(Interestingly it seems as if it has a fully functioning Sprite/Sequence, but is never seen because of 255 Effect)/Demolish/Disrupt
23 - Cure 2/Asura1/
24 - Cure 3/Heal Staff/Asura2/Remedy
25 - Bio
26 - Charm
27 - Weak/(Enemy)Weak
28 - Fatal/Count
29 - Heal/Silver Staff/Staff/(Enemy)Heal/(Enemy)Heal(2)
30 - Peep/Search (overrides Pointer 2)
31 - Life1/Asura1
32 - Life2 (There's a difference?)
33 - Size/Breath/Whisper/Poison
34 - Float
35 - Hold/Entangle
36 - White/Nuke/(Spell)Jinn/MegaNuke
37 - Quake/Titan/(Enemy)Quake
38 - Powder/Digest/Pollen/
39 - Stone/(Summon)Roc/Ray/Beak/Petrify/Hug
40 - (Spell) Indra
41 - (Spell)Chocobo
42 - (Spell) Shiva
43 - Meteo/Comet/(Summon)Bahamut/W. Meteo (even though Pointer 2 seems to handle most of it)
:edit:What this actually seems to do is prevent the graphic from showing on the target and lets Pointer 2 handle the process.
44 - (Spell) Bomb/(Summon)Bomb/Explode/Reaction/Explode(2)
45 - (Summon) Indra
46 - Cure 4
47 - Flame
48 - Flood
49 - Smoke
50 - Pin
51 - (Enemy Spell)Charm
52 - Needle
53 - (Summon)Jinn
54 - Fire/Blaze
56 - Cold Mist/D.Breath/Blizzard
57 - Venom
58 - Hatch
59 - (Summon)Sylph
60 - Blitz
61 - (Summon)Mist (Pointer 2 seems to override this though, 61 on its own seems to be the Sylph Healing graphic)
62 - Maser/Beam/Laser/Heat Ray
63 - Magnet
64 - Fission/Big Wave/Wave(I believe it may be overridden by Pointer 2)

It is. The Sequence looks to be completely unused. It seems to be an explosion from the center-left of the screen that first expands and then moves horizontally.
65 - Counter
66 - Nothing?
67 - Big Bang
68 - Alert
69 - Globe199
70 - Tornado
71 - Storm
72 - (Summon)Mage/Bluster/Blast
73 - Hold Gas
74 - Unused Yellow Flashing effect with Sprites around targets.
75 - Glare
76 - Sleep/Tongue/Gas/
77 - Curse/DullSong
78 - Gaze/Slap/Glance/Crush (Though I believe Pointer 2 may disable that.)
:edit:Doesn't appear to do anything on its own.
79 - A sequence occurs where large rotating sprites hit enemies, and this repeats four times.
80 - Sequence (which was a weird green effect on targets) never ended.
81 - The screen turned blue, enemies began to float but the battle still continued on.
82 - A graphic shows on the targets which seems to change and linger for around 10 seconds before ending.
83 - Nothing
84 - Wave of graphic hits target, repeating five times while target flashes.
85 - Same as 80.
86 - Nothing
87 - Like 84, except hits only once.
88 - Same as 80.
89 - Same as 80
90 - Same as 80.
There are a few gaps, but looking at just the game data it shows what is and isn't used. I'll see if I can figure out what the unused sequences look like then.

And that's that. I think that covers Sprite, Sequence, and Effects in an adequate fashion.