"Crack Pairing" is a term used to describe a pairing that doesn't have any evidence supporting them and seem extremely unlikely that pairing is plausible in Canon. For example, the pairing Kendy would be considered a crack pairing because of the lack of communication between each other and other forms of authentication.
Crack Pairings are usually meant to be humorous in their randomness. They are created by pairing up two random characters (ex. Ike and Bebe), and is often considered the result of a challenge, either from someone outside the author or from the author him/herself: "This pairing is completely unworkable, but I bet I can make it work." The name stems from the notion that the author must have been ingesting some illegal substance just to think up the pairing, let alone write it.