Daggers are tiny weapons & and deal 1d4 piercing damage vs. medium creatures, short swords are small weapons & deal 1d6 piercing damage vs. medium creatures. Actually, with the introduction of 3.5, weapon size categories are equal to the size category of the creature it was designed for. Relative weapon size is listed as "Light", "One-Handed" and "Two-Handed", and both a dagger and a short sword are in the "Light" category.
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I don't think that article is long enough to be worth a d6 dagger... Medium sized daggers are d4.