My best option for case fans?

Important point when you choose to add fans: check whether you need 3-pin (Voltage Control) or 4-pin (PWM) type of fan. If you plan to connect the fan(s) to mobo SYS_FAN or CHA_FAN headers and let the mobo control them automatically, you MUST match the mobo header type to the fan type. If your mobo headers are 4-pin, they cannot control the speed of a 3-pin fan; you need a 4-pin fan to connect to mobo 4-pin port.

BIOS fan profiles do work fine with 3 pin fans.

Automatic speed control of a 3-pin fan can only be done by a mobo port operating in Voltage Control Mode, which is what 3-pin ports always do. Any 4-pin port operating in PWM Mode cannot control a 3-pin fan because that mode does NOT alter the voltage supplied to the fan on Pin #2.

On most mobos today, the mobo's 4-pin CPU_FAN port can be configured in BIOS Setup to operate EITHER in PWM Mode or Voltage Control Mode, thus adapting to your choice for this fan. However, for the CHA_FAN ports on the mobo, only SOME offer this flexibility. Many 4-pin CHA_FAN ports can only operate in true PWM mode and hence cannot control a 3-pin fan. There are, however, some mobo makers who have installed "fake" 4-pin fan ports. These actually are 3-pin (Voltage Control Mode) ports only, even though they have 4 pins, and thus they can control either fan type.

The direction they face. If they suck air in, they are intakes, if they blow the air out, they are exhausts. It all depends on how they are mounted.

If you use a Molex connector to plug the fans into the PSU directly, they will run at a 100% all the time. If you do that. they might as well have two pins

How many fan headers does your motherboard have? You can also use a splitter, to run two fans off one header.

You are correct. the CPU_FAN port is intended for the CPU cooling fan, and should only be used for that. Moreover, I think one SHOULD do that - connect the CPU cooler to the CPU_FAN port and let the mobo take control of that fan.

Regarding case fans, though, my alert of Dec 10 said: "If you plan to connect the fan(s) to mobo SYS_FAN or CHA_FAN headers and let the mobo control them automatically,...". Whether the fan has 3 wires (and pins) or 4 is important only for this case.

If you connect your case fan directly to a PSU output two things result:
(a) that fan will always run full speed - the mobo cannot exercise any control over it; and,
(b) the mobo will not receive the fan's speed pulse signal, so there is no way for your system to tell you what speed the fan is running (if you care), or even whether or not it is running at all.

Yep. Called a fan controller. This is a good one http://www.newegg.com/Product/Product.aspx?Item=N82E16811997078, and you can go cheaper for fewer features.

Actually some mobos do both 4pin pwm or voltage control depending on the fan connected

To repeat, see my post of Dec 10/15. Some mobos allow EITHER 4-pin (PWM Mode) OR 3-pin (Voltage Control Mode) by the CPU_FAN port, and SOME even can automate the choice of type, depending on which fan is found to be connected. Others require that you set this option manually. HOWEVER, not nearly as many mobos offer this feature for their SYS_FAN or CHA_FAN ports that are used for case ventilation.

Regarding third-party fan controllers, you need to understand the distinctions between them and mobo-based control systems. A mobo typically has two fan control systems: one for the CPU fan, and another for the case ventilation fan(s). There may be more than one case vent control system available. The CPU_FAN control system also does a few extra monitoring functions to enhance protection of the CPU from disastrous overheating.

Both systems operate in fundamentally the same manner. For each there is a temperature sensor built into some critical component that its fan is cooling. The control loop has a target temperature for this parameter (the target often depends on the exact item - CPU type, for example) and is custom-set when you first enable the system and the mobo detects the CPU type. It also has settings for the minimum and maximum temperatures it works to, and for alarm limits on that temperature. When executing Automatic Control, each of these two loops constantly compares the measured temperature to the target and adjusts the fan speed as that temperature changes in response to workload changes. The key difference between the two control loops is which temperature sensor each uses. The CPU _FAN control system uses a sensor built into the CPU chip itself by it maker; the SYS_FAN or CHA_FAN loop uses a sensor built into the mobo at some point where its maker believes temperature is critical. On a few mobos you are allowed to change which sensor each loop uses because the mobo maker has installed more than one sensor.

Basically, third party fan controllers have no way to access those sensors built into the CPU and mobo. A fancy model such as that linked above by DonkeyOatie addresses that problem by providing you with a set of its own sensors plus some adhesive. YOU must decide where and how to attach those sensors to monitor what you think is important, AND you also must decide what the "Proper" temperature targets for each point are. Now, for the CPU, obviously it is impossible for you to place one of these sensors inside the CPU chip, so you cannot get a good reading on that internal temperature. That is one reason I always suggest you should use the mobo's CPU_FAN port for the CPU cooling system and let it do its automatic control. For case ventilation fans you could place sensors where you thing appropriate and set targets you like, OR you can just use the mobo's SYS_FAN or CHA_FAN ports and automatic control features. By the way, that particular fan controller unit can handle up to 10W per channel, which is the SAME as the limit on a mobo port (max 1 amp at 12 VDC), but it does offer five separate channels, more than most mobos offer. You should know, however, that some people have found that attaching the temp sensors and getting them to stay there is difficult. Moreover, sometimes the controller's software is buggy.

That controller above is pretty fancy with automatic controls and its own temperature sensors. MANY less expensive ones exist that do NOT have those features. The lower-priced controllers typically only allow you to set the speed of each fan manually. That is, for each control channel you must use a knob or digital buttons to set a speed as you see fit. So that makes YOU the brains of the controller, needing constantly to check some temperature sensor already in the mobo and alter the related fan speed. More often, what people do is set the speeds high enough they never have to take the time to check. Some of the low-priced ones actually will display the speed of the fan you are controlling (IF it is 3-pin or 4-pin and can report its own speed), but the lowest-priced ones do not have even that feature.

The main advantage of third-party fan controllers is that they give YOU total control of fan speeds and cooling. If you want that control, you also must accept you are taking on the responsibility of making sure the cooling is right at all times.

I know this is pretty late to comment on this, but isn't AF fans are for exhaust, and SP fans are for intake?

AFs are designed to move air, but can't handle back-pressure as well, SPs are for moving less air, but preventing air going back out through them. The OP's configuration is a negative pressure case, I think, which is why I made that recommendation. If it were a positive pressure case, then I'd have SPs as intakes and an AF as exhaust.

SPs are also used for radiators in and against graphics cards, where nearby obstructions produced back-pressure.

so that's why my graphics,motherboard and hdd are hot AF. I use SP for front intakes , and top as exhaust.
case : NZXT S340.

I just order 2 Corsair AFs the other day. They should arrive in a couple of days.