Here are my two current setups for macro.
#1 Nikon D300, Micro-Nikkor 105mm f2.8 AF on a Nikon PN-11 52.5mm tube, SB-600 or 800 on a DIY bracket attached to the tripod collar of the PN-11 tube. Allows rotation all the way round the lens axis.
#2 Panasonic FZ50 m4/3 with builtin 12X optical zoom lens and a Raynox DCR-150 +4 diopter attached. Onboard flash is snoot-diffused.
I shoot handheld all the time. Nothing against tripods, I just find greater flexibility and freedom shooting handheld. Starting out settings: F/11, 1/250, base ISO.