Kalahari Air Services is based in Gaborone. Fleet KingAir B200, 1900 and Cessna 210.
Safari Air is aparently based in Maun. Operates single engined Cessna 206's, 207's, 210's and twin engined Britten Norman Islander.
Link (not their site, but has some info): www.desertdelta.co.za/Botswana_Travel_Articles-travel/safari-air-botswana.html
Tanganyika Flying Co. is based in Arusha, Tanzania. Apparently flying Grand Caravans and maybe C206.
Link (not very useful): www.tanflyco.com