This example creates a villager that sells what a traditional PokeMart would sell: pokeballs and some basic medicine. He accepts emeralds and emerald blocks as currency. You can even sell back the items he sells. You can copy and paste this right into a command block (it'll ignore the tabs and returns for you).
/summon Villager ~ ~1 ~
{Invulnerable:1,
Offers:
{Recipes:
[{maxUses:1000000,buy:{id:133,Count:2},sell:{id:4211,Count:1}},
{maxUses:1000000,buy:{id:133,Count:3},sell:{id:4212,Count:1}},
{maxUses:1000000,buy:{id:133,Count:4},sell:{id:4213,Count:1}},
{maxUses:1000000,buy:{id:133,Count:1},sell:{id:4492,Count:1}},
{maxUses:1000000,buy:{id:133,Count:2},sell:{id:4493,Count:1}},
{maxUses:1000000,buy:{id:133,Count:3},sell:{id:4494,Count:1}},
{maxUses:1000000,buy:{id:133,Count:5},sell:{id:4495,Count:1}},
{maxUses:1000000,buy:{id:133,Count:8},sell:{id:4500,Count:1}},
{maxUses:1000000,buy:{id:133,Count:1},sell:{id:4475,Count:1}},
{maxUses:1000000,buy:{id:4211,Count:1},sell:{id:388,Count:8}},
{maxUses:1000000,buy:{id:4212,Count:1},sell:{id:133,Count:1}},
{maxUses:1000000,buy:{id:4213,Count:1},sell:{id:133,Count:2}},
{maxUses:1000000,buy:{id:4492,Count:1},sell:{id:388,Count:3}},
{maxUses:1000000,buy:{id:4493,Count:1},sell:{id:388,Count:6}},
{maxUses:1000000,buy:{id:4494,Count:1},sell:{id:133,Count:1}},
{maxUses:1000000,buy:{id:4495,Count:1},sell:{id:133,Count:3}},
{maxUses:1000000,buy:{id:4500,Count:1},sell:{id:133,Count:5}},
{maxUses:1000000,buy:{id:4475,Count:1},sell:{id:388,Count:5}}]
},
Profession:4,
Career:5,
CareerLevel:5,
CustomName:"PokeMart"
}
Giving an explanation of how this works: After specifying what you want to summon (Villager) and at what location (in this case, one block above the command block), you can further customize the Villagers attributes, including what it buys, sells, what skin it has, and what name it has. I have made him invulnerable just so you won't lose your PokeMart clerk to stray zombies if you enable mobs, but you should really fence him off anyway so he doesn't wander away either. Offers and Recipes represents items that he buys and sells. MaxUses is set to a ridiculous number so it is essentially infinitely available. The buy value is what you give him in exchange for the related sell value (so in case of the first one, you give him two emerald blocks for one pokeball). I'm no economist so the prices I have set here may or may not be totally fair. Profession changes the category, but for all intents and purposes, it's just for specifying the skin when it comes to custom shops. Career and CareerLevel are set to "invalid" values (5 and 5 work for all villager Professions) to keep the villager from making new offers and potentially erasing your custom ones. And finally, the CustomName attribute will assign the name you want.
Given how long it can take to make pokeballs, and healing items are hard to come by, I'd say take some time to establish some shops like this one if you want to add a little bit of economy to your Pixelmon world since it might be a while before we see PokeMarts added to the mod officially. It's completely native to Minecraft 1.7, so no extra mods are required. If you want to get into doing more custom Villager shops, I recommend searching for tutorials online and reading up on how command blocks work, but the best way to learn is to play with commands.