Armor of God (CC, p 48): Lose a bonus feat. As a immediate action, lower your will save to +0 and add your normal bonus to your AC.
Armored Mage (CM, p 32): lose medium and heavy armor, can pick an arcane class and cast in light armor, but only spells level equal to your fighter level +1.
Aligned Strike (CC, p 48): lose bonus feat, gain ability to align your weapon.
Counter Attack (PHB 2, p 45): Lose bonus feat. Use a full round action to make an attack, when you're attacked during that round you may attack your attacker as an immediate action.
Darksong Knight Substitution Levels (CV, p 38): d8 HD, add Perform (dance)
2nd level: Dancing Feint (use Perform (dance) to feint)
6th level: Favored Enemy (yochlol)
8th level: Combat Dancing (+2 dodge bonus against AoOs, +2 attacks using Spring Attack)
Dragonscale Husk (DrM, p 12): lose armor proficiency, gain scaly hide.
Drow Fighter (DU, p 58): Gain +2 initiative and Dex to damage against flat-footed enemies, lose heavy armor and tower shield proficiency.
Dungeon Crasher (DS, p 10): lose bonus feats, gain bonuses to break doors and traps. Gain a bonus on bullrush and do extra damage.
Dwarf Fighter Substitution Levels (RS, p 146): d12 hitdice, gain knowledge: dungeoneering
1st level: Axe Focus (+1 attack with axes), lose feat
2nd level: Racial Foes (+2 damage vs orcs, goblins, and giants), lose feat
8th level: Heavy Armor Expertise (+1 AC in heavy armor), lose a feat
Elusive Attack (PHB 2, p 44): Lose bonus feat. Make a full round action to make one attack and gain +2 dodge bonus to AC, increases with levels.
Half-Elf Fighter Substitution Levels (RD, p 157): d8 hitdice, extra skills
1st level: Blade focus (+1 attack with longsword and rapier), lose a feat
2nd level: Main Gauche (AC bonus from TWF), lose a feat
6th level: Confusing Banter (bluff or diplomacy check while fighting to add to attack), lose a feat
Kobold Fighter Substitution Levels (RDr, p 108): gain profession: miner and search
1st level: Spear focus (+1 attack with spears), Dodge. Lose bonus feat, medium, and heavy armor proficiency
2nd level: Constitution Boost (+2 Con), lose feat
4th level: Strength Boost (+2 Str), lose feat
Overpowering Attack (PHB 2, p 45): Lose bonus feat. Make a full round action to make one attack which deals double damage.
Planar Fighter (PlH, p 32): gain knowledge: the planes as class skill
4th level: Planar Study (+2 bonus damage vs outsiders and extraplanars), lose bonus feat
8th level: Align Puissnance (make weapon aligned), lose bonus feat
12th level: Aura of Stability (dimensional anchor on self), lose bonus feat
Raptorian Fighter Substitution Levels (RW, p 161):
1st level: Encumbered Flight (can carry medium load flying), lose heavy armor weapon proficiency
4th level: Airborne Strike (+2 damage when flying higher than opponent), lose feat
8th level: Fast Flight (+10' to glide speed), lose feat
Resolute (CC, p 48): lose a bonus feat. As an immediate action, reduce your BAB by half and add that amount to your will save.
Stealthy (UA, p 58): Lose bonus feats, gain sneak attack.
Thug (UA, p 51): No first-level bonus feat, only light armor. Extra class skills, adds Urban Tracking to bonus feat list
Warforged Fighter Substitution Levels (RE, p 130): d12 hit dice. Add craft and intimidate to class skills
1st level: Battle Hardened (+3 to initiative checks and saves vs fear), lose bonus feat
2nd level: Bonus Warforged Feat, replaces fighter feat
4th level: Body as Weapon (+2 damage with slams or warforged weapons), lose bonus feat
Zhentarim Figher Substitution Levels (CV, web): Add bluff and diplomacy to class skills.
3rd level: Bonus Feat: Skill Focus(intimidation)
5th level: Extended Intimidation: intimidation lasts longer
9th level: Swift Demoralization: intimidate as a swift action
And yet, a Fighter is still better than a Barbarian.