Seriously though, it depends. If you have no other way to intake or exhaust air, probably 3, since fans are more effective at blowing than sucking. (IE: 1. would spend some of its power recirculating inside and outside air rather than just pulling inside air out.)
Most likely your bathroom and hopefully stove have exhaust fans, so even better would be to turn one or both of those on, and have the fan blow in a window on the opposite side of the house. It may not even be ideal to open all the windows. You want cool air flowing through the whole house. In an extreme example, if you have the fan blowing in the balcony and an open window right beside the balcony, it could just circulate air there, rather than reaching the rest. Likewise with exhaust, if you have a fan in the bathroom and the bathroom window open. So you'd need to experiment a bit to see what flows air best through the house.
I had a similar problem in my previous house which didn't have central AC. The insulation in the house was great for about one day. But in an extended heatwave, outside 100F meant eventually inside 90F.
I got decent cooling results with two separate window fans, opposite sides of house, one blowing in one blowing out. Of course, all other windows are closed.
A single window fan of the above style can cool a single room quite well, blowing cool air in and blowing hot air out.
As others have mentioned, depending on breeze and temperature, opening all the windows can sometimes work better than multiple fans.
Fans are just no substitute for a real AC unit, which can lower indoor air temp to below outside air temp and can also extract moisture from the inside air.
Another suggestion from your 3 - use an exhaust fan on one end of your home, blowing air from your ceiling out a window(you want to blow the air near the ceiling, it is warmest). Use an intake fan at the lowest elevation possible.
The premise is...cooler air falls, warmer air rises. You want to blow in the low(cool) elevation air, and exhaust the high(warm) air.
I wonder the same thing. If you get a chance, try to test the various configurations!
I would suspect you will also see different results depending if you have multiple windows or just 1. For example, if you have more than 1 window and can seal the opening except the fan, then the fan will move x amount of air in or out and will have similar results.
Simply mixing the air inside the room seems like it's probably the least effective because it will result in very little heat exchange at the windows themselves. However, making the temperature within your house more even may make it more comfortable on the average inside your house.
Given that I only have one portable fan, what is the best setup at night if it is colder outside than inside:
1. Open the windows and put fan so that it blows air out of one window
2. Open the windows and have fan mix the air inside the room
3. Open the windows and put fan on balcony to blow air from outside in.