Antiquarian (CC, p 51): Lose trapfinding. Gain wisdom bonus on appraise checks with divine items. Can attempt to identify divine items, as per the spell.
Breathstealer (DrM, p 11): Pick as one of your special abilities. Use sneak attack to prevent a dragon from using its breath weapon.
Changeling Rogue (RE, p 121): Add one knowledge skill to class list, 10 skills per level
1st level: Social Intuition (grants bonuses to a number of social skill checks), lose trapfinding
3rd level: Minor Lore (+1 to knowledge checks, +1 every 3 levels), lose trap sense
8th level: Mutable Anatomy (50% chance to negate extra damage from a critical or sneak attack), lose uncanny dodge
Death's Ruin (CC, p 51): Lose trapsense. Can use sneak-attack on undead, at one half normal.
Disruptive Attack (PHB 2, p 57): Don't gain uncanny dodge. Whenever you attack a flanked or flat-footed target, you can sacrifice your sneak attack to give them a -5 to AC.
Drow Rogue (DU, p 58): Gain poison use, lose trapfinding.
Feign Death (EoE, p 21): lose evasion, gain ability to appear dead Friend's Evasion (CC, p 51):
Lose improved evasion as a special ability option. Every ally adjacent to you gains evasion.
Frostfell Terrain Mastery (FB, p 45): +2 initiative and +10 land speed in cold terrain, gained as special ability.
Golden Hands of Vergadain Substitution Levels (CV, web): must be a dwarf; add Survival to class skills
2nd level: lose +1 to Reflex save from your level, get FE bonuses vs a certain organization.
3rd level: gain Track, lose trap sense. Gain bonuses to tracking in place of trap sense
6th level: lose the BAB bonus from the level, gain Urban Tracking
Goliath Rogue Substitution Levels (RS, p 152): d8 hitdice, add survival to class skills
2nd level: Mettle of Mountains (+4 bonus to For, Mettle), no evasion
3rd level: Wild Sense (bonus to knowledge: nature checks), lose trap sense
8th level: Fortification (25% chance to prevent crits and such), lose uncanny dodge
Halfling Rogue Substitution Levels (RW, p 160)
1st level: Ranged Sneak Attack
3rd level: Thief's Luck (can reroll reflex saves), lose trapsense
10th level: Sniping Mastery (can take ranged attacks while hiding), lose special ability
Holy Stalker (CC, p 51): Lose crippling strike as a special ability option. Add two points of damage per normal sneak attack dice when sneak attacking undead.
Kobold Rogue (RDr, p 109): d4 hitdice, add knowledge: dungeoneering to class list
1st level: Rapid Retreat (+5' while withdrawing), Shrewd Trapfinding (+2 bonus to find/disable traps)
3rd level: Improved Trap Sense (bonus to saves vs. traps), Shrewd Trapfinding
8th level: Evasive Skitter (can move out of area of effects), Shrewd Trapfinding
Lightbringer Penetrating Strike (ECR, p 208): When flanking a creature normally immune to sneak attack damage you still deal half your sneak attack dice in damage. Does not effect creatures immune to flanking, and can only be used against flanked creatures.
Martial Rogue (UA, p 58): Lose sneak attack and gain bonus feats as a fighter.
Mimic (EoE, p 21): lose trapfinding, gain disguise self
Penetrating Strike (DS, p 13): Lose trap sense. Whenever you sneak attack something normally immune to sneak attack damage, do half your normal dice of sneak attack damage.
Planar Rogue (PlH, p 34): gain knowledge: the planes as a class skill
6th level: Breach Sense (detect activation of portals and spells that cross planes)
10th level: Slip the Bonds (turn ethereal once per day), replaces normal special ability
16th level: Blink once per day, replaces normal special ability
Quick Fingers (DS, p 13): Lose one level of trap sense to reduce the time needed to disarm traps.
Rilkan Rogue Substitution Levels (MoI, p 47): add speak languages to class skills
1st level: Improved Flanking (+4 bonus while flanking), lose one die of sneak attack
3rd level: Bardic Knowledge, Bonus feat, lose trap sense
10th level: Fortunate Reflexes (reroll reflex saves), replaces normal special ability
Spell Reflection (CM, p 35): Lose evasion, gain the ability to reflect spells targeted at you that miss.
Spell Sense (CM, p 35): Lose trapsense. Gain AC bonus vs spells.
Wilderness Rogue (UA, p 56): Modified skill list. Add camouflage, woodland stride, and hide in plain site to the list of abilities rogues can pick.
Uncanny Bravery (DrM, p 14): Gain immunity to draconic presence and resistance to fear instead of uncanny dodge.