Whitaker was taken by the Friars in the 27th round of 2002, notching a 29-38 record with a 3.25 ERA over four seasons in the system. He had his worst year in 2005 when he went 8-13 with a 4.33 ERA.
Cassel was selected in the 25th round of the 2000 draft by the Padres, compiling a 26-29 record with a 4.06 ERA over 272 games.
Thayer, who led the Southern League in saves and has recorded 75 saves over the last three seasons, returns to Mobile despite posting a 2.34 ERA for the BayBears in 2005.
Jones has been in the system since being selected in the 32nd round of the 1998 draft. The lefty went 3-5 with a 4.37 ERA last year in 55 games for the BayBears.