Outside of Complete Scoundrel (14) and Sharn: City of Towers (168), the prestige class exotic weapon master is unmentioned beyond its original appearance in Masters of the Wild (53–4) then its revised appearance in Complete Warrior (30–1). Neither Scoundrel nor Sharn offers anymore insight than Warrior into how to use the exotic weapon master prestige class's extraordinary ability exotic weapon stunt (uncanny blow). That means you're stuck reading the special ability and making a choice.
What uncanny blow says…
The extraordinary ability exotic weapon stunt (uncanny blow) says
When wielding a one-handed exotic melee weapon in two hands, the character can focus the power of his attack so that he deals extra damage equal to his Strength bonus ×2 instead of his Strength bonus ×1-1/2. If he has the Power Attack feat, he treats the weapon as two-handed for purposes of determining his bonus on damage rolls. (31)
(If that last sentence strikes you as a largely unnecessary reminder, it should. This reader suspects that the precise wording of the 3.5 revision's of the feat Power Attack (PH 98) was still being decided when Complete Warrior was published, Warrior appearing on shelves only 5 months after the revised Player's Handbook.)
Anyway, the Player's Handbook description of the bastard sword, in part, says, "A bastard sword… is an exotic weapon. A character can use a bastard sword two-handed as a martial weapon" (121). And the bastard sword appears on Table 7–5: Weapons under the heading Exotic Weapons under the subheading One-handed Weapons (117). For this reader, that's enough: the bastard sword is always a one-handed exotic weapon that can—it just so happens and if the wielder so chooses—also be used as a martial weapon if the wielder employs it two-handed.
Thus this GM would rule—perhaps even a little reluctantly, depending on the optimization level of the campaign and the possible outcome of such a ruling—that a creature that's proficient with all martial weapons, that enters the prestige class exotic weapon master, and that picks the special ability exotic weapon stunt (uncanny blow) can use that special ability with a bastard sword that the creature wields in two hands, despite the creature not possessing the feat Exotic Weapon Proficiency (bastard sword) (PH 94) yet possessing the feat Weapon Focus (bastard sword) (PH 102) (perhaps through a workaround like the swordsage's extraordinary ability discipline focus (Weapon Focus (Diamond Mind)) (Tome of Battle 16).
…Then there's some Sage Advice
The Dragon #316 Wizards Workshop column "Sage Advice: Equipment and Combat Official Answers" (100–4) includes two exchanges relevant to the extraordinary ability exotic weapon stunt (uncanny blow).
So when is a weapon “two-handed?”…
Table 7–5 in the Player's Handbook lists weapons as light, one-handed, or two-handed strictly as a matter of convenience. These size categories [i.e. the effort required for a creature to wield the weapon] are always relative to the wielder’s size….
When the combat rules speak of “two-handed” weapons, they’re referring to how the weapon is being used. A Medium character using a Medium longsword in two hands is using a “two-handed” weapon. The same character using a Medium lance in one hand while mounted is using a one-handed weapon. (101–2)
So, according to this advice, a creature that's wielding a bastard sword in two hands is using that bastard sword as a two-handed weapon. That means the special ability exotic weapon stunt (uncanny blow) can apply to the bastard sword, and we're good to go, right? Not so fast. The very next question is this one:
Exactly when is a weapon light, one-handed, and two-handed?…
The bastard sword, lance, and dwarven waraxe are all two-handed weapons that can be used in one hand under the correct circumstances (the bastard sword and dwarven waraxe are shown on Table 7–5 as one-handed exotic weapons, but they’re really two-handed weapons). Treat all three of these weapons as two-handed weapons when determining who can use them and how. For example, a Small character cannot use a lance or bastard sword made for a Medium creature, even when mounted (in the case of a lance) or when the Small character has the Exotic Weapon Proficiency (bastard sword) feat. (57)
(Emphasis in answers mine. The Sage at the time is Monster Manual primary author and dnd-3e co-designer Skip Williams.) So, in sum, the advice tells the reader that Table 7–5: Weapons lists the bastard sword and dwarven waraxe as one-handed weapons only for convenience and that outside of combat, those weapons are totally two-handed weapons, even though in combat those weapons can be considered either one-handed or two-handed weapons depending on how they're used.
So an argument can be made either way. On one hand, the description of the stunt uncanny blow could be describing how a creature must be using the exotic weapon in combat, so the stunt totally falls under the first ruling, making using the stunt with a bastard sword that's used two-handed legit. On the other hand, the description of the stunt could be describing in the abstract the kind of weapon that the creature must wield to experience the stunt's bonuses, and that description is independent of the weapon's wielder, in which case the stunt's not legit for use with the bastard sword or dwarven waraxe because, technically, no matter how they're used those weapons are always two-handed weapons.
This reader tends to favor the former rather than the latter: the universe is hard enough on the mundane warrior without—as it seems to this reader—double-secret rules prohibiting players from their PCs being ever-so-slightly improved and more versatile axeman or swordsman.
Note: These Sage Advice exchanges are repeated nearly verbatim by the Main FAQ on pages 48 and 57, respectively. Issues with the FAQ can be viewed in answer to this question.