BEECH 95 (N9750Y) WAS TRACKING SOUTH AT APRX 185 KTS AS CESSNA 180 (N42695) WAS TRACKING 118 DEG AT ABOUT 147 KTS. BOTH WERE IN VMC, RCVG RADAR SVC (VFR FLT FLWG) FM STOCKTON TRACON. DRG AUTOMATED RADAR HANDOFFS TO TRACY SECTOR (TR) CTLR, THE PLTS RPRTD AT 5500' MSL. SUBSEQUENTLY, THE 2 ACFT CONVERGED, COLLIDED AT ABOUT 5500' MSL, THEN CRASHED IN UNCTLD DSCNTS. THE CTLR WAS OCCUPIED WITH CTLG 2 OTR ACFT. BOTH WERE OPERG UNDER IFR & REQUIRED HIS ATTN TO MAINT SEPN. THE COLLISION OCCURRED AS THE CTLR WAS CONCENTRATING ON SEPN OF THE 2 IFR ACFT. N9750Y CONVERGED ON N42695 FROM THE NE (APRX70 DEG LEFT OF N42695'S NOSE). N42695 CONVERGED ON N9750Y FM THE SW (APRX 48 DEG RGT OF N9750Y'S NOSE). THE CTLR WAS NOTAWARE OF THE COLLISION UNTIL LATER. THE STOCKTON ARTS II RADAR WAS NOT EQUIPPED WITH A CONFLICT ALERT SYS. THE ARTS II RADAR WAS PROGRAMMED TO MOVE NO BEACON (VFR) CALL SIGNS TO THE TAB LIST AFTER NOT RCVG A TRANSPONDER REPLY FOR 5 SCANS (APRX 20 SEC). AFTER AN ADNL 33 SCANS (A TOTAL OF APRX 2.5 MIN), THE CALL SIGN WOULD DISAPPEAR FM THE TAB LIST, AS WELL.