I've currently got the following systems:
Craftsman C3 19.2v
Hitachi 12v LiIon
I've got the most tools for the Craftsman (drill, circular saw, jigsaw, spiral saw, light) and they are good. I don't have issues with the circ saw as I realize it's a battery saw. It's good for what I use it for - cuts of 2x material, the occasional plywood sheet, etc. I'd say get the big LiIon battery - it really wakes that saw up.
That being said, I'm probably going to switch to the Milwaukee 18v as the Craftsman stuff dies off. Their system has good capabilities and they seem to have better made tools and are staying on top of the game on them. Craftsman seems to be moving away from the C3 line.
Hitachi 12v were bought because I wanted an impact driver and at under $100 for a impact driver, drill, and light, it was a steal. It's a decent set but the drill is gutless. The driver rocks though. It's my "spare" set.
I started the Milwaukee 12v system as I wanted a multitool and hammerdrill. Picked up the Hammerdrill, multitool, and impact last Black Friday at Home Depot. I love this set - it's the one I reach for most. The hammerdrill is handy for tapcons and smaller sized holes. It's got decent torque (won't drive a 3" lag screw but comes very close) and works well. Impact driver rocks and the multitool is top notch. I added a right angle drill to it and it also works awesome. Milwaukee is coming out with plenty of 12v tools so that's a bonus!
If I had to do it over again it would be Milwaukee 12v and 18v all the way. The new Fuel stuff looks awesome and they make a charger that charges both their 12v and 18v batteries.