Spoiler: Metamagic Arcane Thesis +0 3rd level
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Alternative Source Spell (Dragon #325): For the cost of 1 caster level, and one slot from a class that grants the spell, you can prepare an arcane spell as divine, or a divine spell as arcane.
Black Lore of Moil (Complete Arcane, page 76): Any Necromancy spell deals +1d6 damage, +1d6/two spell levels. Must expend a 'runebone' that costs 25gp per 1d6 to be generated. See feat for full details.
Born of Three Thunders (Complete Arcane, page 76): Any [electricity] or [sonic] spell that deals damage has its damage split split 50/50 between electricity and sonic damage. Adds Fort save or deafened, plus Reflex save vs being knocked prone.
City Spell (Cityscape, page 59-60): Any spell with an energy descriptor and cast within any urban area above the size of small town converts 50% of its damage into "city" damage.
Cooperative Spell (Complete Arcane, page 77): Requires additional person with this feat, who casts the same spell with you. Adds +2 DC and +1 caster level to beat Spell Resistance, and uses the better of the two spellcasters' DC and caster level. Can be expanded into multiple extra people, adding +1 DC and +1 CL for each additional person.
Energy Affinity (Miniature's Handbook): Subsumed by Energy Substitution; also slightly harder to qualify for. Same effect.
Energy Substitution (Complete Arcane, page 79): Any spell with an energy descriptor can be changed to have the energy descriptor (and deal corresponding damage type) chosen by this feat.
Ghost Touch Spell (Ghostwalk, page 34): Allows spells to affect ghosts and only ghosts.
Imbued Healing (Complete Champion, page 60): Adds a rider effect specific to one of your domains on the tail-end of your conjuration (healing) spells. Has a table for non-PHB domains on page 53.
Invisible Spell (Cityscape, page 61): Removes all visual manifestation of a spell.
Lord of the Uttercold (Complete Arcane, page 81): Any spell with the [cold] descriptor can be changed to deal half cold damage, half negative energy damage.
Miser With Magic (Kingdoms of Kalamar Player's Guide, page 88): Not really a metamagic feat, despite being marked as such. After casting a spell, make a Spellcraft check at a DC = 10+(2* Spell Level). Succeed, and you get the spell back. Fail by 5 or more, you don't cast it and lose the slot. Regains a number of spell levels equal to your primary casting stat modifier.
Sanctum Spell (Complete Arcane, pages 82-83): Has an effective spell level of +1 when cast in sanctum, but -1 cast outside of sanctum.
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Bend Spell (Dragon #291, Dungeon Compendium Vol. 1): Negates cover bonuses.
Blistering Spell (Player's Handbook II, page 91): +2 fire damage per spell level, and -2 to attack rolls and checks if the target fails its save. [fire] spells only.
Clawed Spell (Dragon #315): Spell deals 1d6 Force damage for every 5 caster levels.
Coercive Spell (Drow of the Underdark, page 47): Spell deals a -2 penalty to Will saves for 3 rounds, non-cumulative.
Consecrate Spell (Book of Exalted Deeds, page 42/Complete Divine, page 79): Spell gains [good] descriptor, and if it deals damage, half of it is divine damage.
Corrupt Spell (Book of Vile Darkness, page 47/Complete Divine, pages 79-80): Spell gains [evil] descriptor, and if it deals damage, half of it is divine damage.
Deafening Spell (Drow of the Underdark, page 49): Any spell that deals damage also deafens its target for 1 round. No save.
Deceptive Spell (Cityscape, page 60): Makes a spell appear to originate from a different direction.
Energize Spell (Libris Mortis, page 26): Deals 1.5x damage to undead creatures, but 0.5x damage to non-undead and objects.
Enlarge Spell: Doubles the Range entry on a spell's description.
Extend Spell: Double duration of a spell.
Fell Energy Spell (Dungeon Compendium Vol. 1, Dragon #312): Any spell that gives a numerical bonus gives an extra +2 to undead.
Fell Weaken (Libris Mortis, page 27): Any spell that deals damage also deals out a non-cumulative -4 Strength penalty.
Fiery Spell (Sandstorm, pages 49-50): Only usable on spells with the [fire] descriptor, adds +1 damage per die of damage dealt by the spell.
Flash Frost Spell (Player's Handbook II, page 91): Only usable on spells with the [cold] descriptor, adds +2 damage per level of the spell and creates a quasi-grease effect in the spell's area for 1 round. Note that any spell when using the Snowcasting feat is a [cold] spell.
Forceful Spell (Dragon #358): Adds a Save-or-Suck to any spell on any one target (even on an area-of-effect spell): Save or be knocked prone and stunned for 1 round.
Imbued Summoning (Player's Handbook II, page 92): Any creature created by conjuration (summoning) spells can have any spell you know of 3rd level or lower with a range of touch cast on it auto-magically.
Sculpt Spell (Cityscape, page 63, Complete Arcane, page 83): Changes an area spell's area.
Silent Spell: Removes Verbal components.
Still Spell: Removes Somatic components (and arcane spell failure for armor).
Transdimensional Spell (Complete Arcane, page 84): Allows a spell to affect an incorporeal creature, creatures on the Ethereal Plane or Plane of Shadow, and creatures within an extradimensional space within the spell's area.