Almost all transactions are electronic and 'numbered accounts' held by various gnomes of zurich are ubiquitous and used by shadowrunners, corporations and private citizens. When a corporate johnson pays he'll hand over the exclusive access key for a numbered account which the runner will change, then drain the account into another anonymously held account, then close the account given to him by the Johnson.
Such numbered accounts will also also handle corp scrip for a fairly nominal fee (I bundle it as part of your lifestyle costs, my runners pay medium or high, and this service is included. If one of them was squatter I might actually do something about it).
However, runners often deal with other weird people, such as vampires, the triads and the yakuza and chinese warlords, who may do somethign completely different. For example, the vampires might hand over some magical artifacts, the yakuza will probably pay with a mix of black money like a johnson and quid pro quo, and a chinese warlord has access to bits of kit and will hand that over, or esoteric artificants that the players then go on to sell (fairly legitimately) to auction houses. The houses take a big cut to assure themselves of providence and then run with it.