Rakistan is a fictional country known to be hostile and participate in manufacturing chemical weapons.
In episode #290: “A Name, Not a Number, Part 1” it is mentioned that Rakistan commissioned the creation of the deadly Ruku Virus which was subsequently hijacked by the terrorist organization Red Scorpion. Upon the theft of the Ruku Virus, the scientist responsible for the creation of the virus was "disposed of" by the Rakistani government. Based on the name and mentioned activities in the episode it can be inferred that Rakistan might be a former Soviet republic, an Arabic country or a combination of the two.
In #514: “Room Enough for Two”, Mark Horton's army unit is called to deployment in Rakistan when hostilities break out in the country. By the end of the episode hostilities had subsided and Mark informed his family that his unit would be returning from their deployment soon. While Mark did return home, in episode #557: “A Lamb's Tale” he has a broken leg and mentioned a fallen comrade sacrificed his life to save Mark's, however it is not stated whether this incident took place in Rakistan or whether Mark was deployed to another hostile region. Based on the release date it can be inferred that the writers created the war in Rakistan as a metaphor for the war in the real life country of Iraq. It can also be assumed that it is also meant to be Afghanistan or perhaps a combination of the two.