The Top-14 team, who have qualified for next season's Heineken Cup, also added versatile Argentinean front rower Eusebio Guinazzu, 24, from Toulon.
Prop Van Niekerk, 28, and lock Stoltz, 31, both signed from Super 14 team the Cats while 27-year-old Badenhorst came from their rivals the Stormers.
The foursome join other recent signings, New Zealander Keith Meeuws, Samoans Ace Tiatia and Rambo Tavana as well as Thomas Soucaze, Peio Som, Arnaud Mignardi and Laurent Cabarry.
This is the second time that Agen have qualified for Europe's premier club rugby competition. Agen's Heineken Cup opponents in Pool 2 will be Gloucester Rugby, Edinburgh Gunners and the 2006 semi-finalists Leinster.
Other Heineken Cup Pools 2006/07:
Pool 1: Trévise, Perpignan, London Wasps, Castres.
Pool 3: Sale, Stade Français, Calvisano, Ospreys.
Pool 4: Cardiff, Bourgoin, Leicester, Munster.
Pool 5: Ulster, Toulouse, London Irish, Llanelli.
Pool 6: Biarritz, Northampton, Parme, Border Reivers.