Can a cleric use the skill Craft (cooking) when casting create food and water to attempt to create better tasting food and water? Similarly, can a wizard use the skill Craft (cooking) when casting Mordenkainen's magnificent mansion to attempt to create a better banquet within the mansion? Also, can the Craft (cooking) skill be used to change a magic potion's flavor?
Unless the DM agrees, the skill Craft is likely no help when casting the spell create food and water, which explicitly creates "simple fare of your choice—highly nourishing, if rather bland" and water that's "just like clean rain water" (PH 214-5). Mordenkainen's magnificent mansion says only that it creates a "nine-course banquet" (PH 256), but given how the mansion's described otherwise, I expect this to be already high-quality grub not, like, nine courses of soda crackers and lime gelatin. (As DM I have allowed the mansion's caster to dictate the culture of the fare created within a mansion—blowing a 7th-level spell on improved rope trick should have some advantages.) How potions and poisons taste is really up to the DM—the potential to weaponize either by falsifying tastes is a real role-playing possibility which a campaign must address individually if ever the need arises.
But, when using the spell fabricate, "[y]ou must make an appropriate Craft check to fabricate articles requiring a high degree of craftsmanship" (PH 229), so a successful Craft skill check might be useful if making raw materials into a gourmet meal in such a fashion.
If you must, like Dan B.'s answer mentions, make food taste different or better using the spell prestidigitation. Alternatively, just make better-tasting food than the create food and water spell can by casting the 2nd-level Clr spell festival feast [conj] (Dragon #342 41), which creates "a meal of good food, wine, ale, and beer [that] smells and tastes wonderful, while being highly nourishing and satisfying to eat."
Note that I'm unaware of a printed example of the Craft skill applied to food. The skill Profession (cook), on the other hand, receives a bonus from the feat Halfling Lore (Dragon #315 53), can be used to make halfling alchemical items taste good from the Dragon #285 article "Walk and Riddle: The Secret Life of Halflings" (38), and can be used to detect the Drow of the Underdark poison The Calling (94-5). Even the best cooking themed adventure—Andy Collins's "Something's Cooking" featuring the infamous calzone golem (PDF now sadly absent from its advertised Web page)—has its NPCs possessing only the skill Profession (cook) and not the skill Craft (foods) (which does explain the absence of a macaroni and cheese golem).
The Craft skill lets you "know how to use the tools of your trade", which presumably includes knowing how to add spices to things, but there are no rules for using it to modify the flavor of a food.
Masking the taste of a poison is quite difficult. Many poisons taste really foul (because your taste buds have identified "this is a poison" and they want to make sure you notice that), and adding flavors won't mask that.
However, you'll want to know about the wizard cantrip prestidigitation, which allows you to perform simple magical effects for one hour. One possible effect is to "chill, warm, or flavor 1 pound of nonliving material". This effect lasts up to an hour.
In a way to add flavor to a game, this is a great idea. As an extension to the rules, this would be a dangerous area to tread into if it makes the saves more difficult or have better effects.
However, its always best to remember that in the end, something like this is a call the GM of that game must make.