Three fans and three Molex connectors, seems there's a capacity limit. BUT there is an easy solution. You can get two-from-one adapters that convert one Molex connector into two. Stack three of them and you can make four-from-one, then you use the Molex-to-fan adapters to connect the fans to those extra Molex supply points. Fans use little power, so you can easily afford to power four from one original Molex connector from the PSU outputs, leaving the other two originals still free.
A fan controller as LePhuronn suggests may be another way, IF that controller has multiple outputs for fans from one Molex supply, and it gives you ability to manually set fan speeds.
Another option if you are handy at soldering is to splice fan wires together so that two or three fans are powered all from one connector plugged into a mobo fan pinout. There are two things to watch for here. One is that you can't really get spec's for how much power the mobo output is prepared to provide to "the fan", so it's hard to know if you are in danger of overloading that pinout. My GUESS is you could easily do this with two fans from one pinout, maybe three, more than that I have no idea! The other is to be careful which wires you splice. A typical fan has three wires - Black for Ground, Red for +12 vdc supply, and yellow for a fan speed signal sent back to the mobo. The mobo's automatic fan speed control uses temperature measured somewhere relevant to vary the +12 vdc supply for fan speed, and then monitors the speed signal (yellow wire) to ensure it is running and display the actual speed if you want to see it. However, it could not possibly figure out fan speed if you were to splice together the yellow leads from three fans! So when you splice, put the Blacks all together, and the Reds all together, but leave ONLY ONE YELLOW lead attached to the fan connector - simply leave the yellow leads from the other two fans not connected to anything. The actual speeds of those two will never be known to the mobo, but it will be happy to tell you about the one yellow lead signal it does get. Meanwhile, ALL (2 or 3) of these fans with Blacks and Reds spliced together will get the same supply voltage and run at the same speeds.
Don't misuse mobo fan connectors. The one marked CPU_FAN MUST be used ONLY for the CPU cooling fan. Likewise, if there's one labeled PWR_FAN, it can ONLY be used for a lead coming out of your PSU for this purpose - many PSU's do NOT have such a connector, so you cannot connect anything to this mobo pinout. Then you will have one, two or more fan pinouts labeled SYS_FAN1, etc. THESE are the ones for case fans. Read your manual carefully. I think mine says the SYS_FAN1 connector actually uses a mobo temperature measurement to control the speed of a fan connected here, but the SYS_FAN2 connector has no speed control system and simply runs full speed all the time. Yours may differ.