Put simply,,, use a 1 or 3 Watt for tight beams that throw more.
Use a 5W for more overall light output, with more of a flood beam, with more spill light.
The 4 die patern of the 5W makes it harder for the reflector or optic to focus. Sence it is actually 4 focal points, even though they are very close together, it still makes it so they can be focused as much as the 1 and 3W leds.
What makes lights brighter than others: hmmm
I would say the 3 most important things are: LED effeciency, mA the LED is driven at, and the optic or reflector used. (in that order)
A good BIN led can make all the differece. Driving a much less effeciant led at very high mA will just make it run hotter, with even LESS efficiency.
The mA (milli Amps) that are sent to the led is basically how hard the led is being driven. 1W leds are rated at 350mA, but all of us drive them harder. Some as high as 1,5 amps!!! But, for the most part, you dont want to go above 700mA. Any more than that will run the led too hot, and you wont get much more light output for the loss in runtime.
3W leds are rated at 750mA. They are basically 1W leds that can take more mA and handle the heat generated by that easier.
5W leds are rated at 750mA also. Many people like to direct drive these. (no converter, regulator, or resistors) This can lead to as much as 1.6 amps going to the led. This is BRIGHT, but you MUST have VERY good heat sinking to do this.
You should always heat sink an led as well as possible, the cooler the led is, the more effecient it is.
If you are driving an led at under 200mA, you dont have to heat sink it. But, it wont hurt to do it anyway.