I use a lot of Molex KK .1" and .156" connectors. They are cheap, flexible and reliable. Cables can be hand-built with low cost tools. However there are several traps involved with these seemingly simple connectors.  There is no published 'standard' for pin 1, Amp and Molex are almost but not quite compatible with each other. there are gold and tin plating, which to use? Should you use straight or right angle? Should you use crimp-and-poke or IDC connectors? And how do you lay out PC boards for them?

Footprints

So where the hell is pin 1?

Molex puts Pin 1 of the male header and pin one of the female housing at opposite ends! What were they thinking?? Amp (aka Tyco, TE...) avoids the issue by not specifying Pin 1 on the male header. But a connector is pretty useless without knowing where pin 1 is!  Additional confusion is provided by not marking the male header with a pin 1 indication. Come on guys!!

I, like most, use the housing standard. Of course, this confuses the PC layout guys. But they only get confused once. Better that than confusing the cable manufacturer forever, every time they build a cable. If you look at DC Fan connectors which often use the 2 or 3 pin KKs, they use the housing convention.

Other Differences between Amp and Molex.

Ramps, keying, etc.

male headers with the keying feature. Life its too short to spend time figuring out how to plug in a cable, or dealing with the smoke and damage caused by plugging in a cable incorrectly. There is only one correct way to plug in a cable, but there are lots of incorrect ways: off by 1, reversed, wrong plug,  The keying feature is there to prevent all of these. It has the other advantage of preventing you from plugging a 5 pin female into the 6 pin housing. True, you can plug the 6 pin cable into the 5 pin male if you're not careful, but then when you go to plug in the 5 pin cable to the 6 pin male,  you will see the error of your ways. Hopefully before you power up the system and damage something.

I generally try not to have two different connectors of the same size in a system. If you must have multiple identical cables that use the same connectors, label both the PCBs and the cables clearly. And make sure your system will not be damaged when you reverse them. You will plug them in wrong, but will eventually learn, the hard way, to match the labels. Murphy says if someone can build it wrong, they will, and at the worst possible time and with the most expensive possible consequences.
The females come with or without the ramps, and with or without the keying features. I use only ramps and keys. They look like this:

I see that a lot of makers like the Dupont style of connectors. They have the advantage of coming in 1 and 2 rows, and the connectors are only 0.1" x 0.1: per pin, no extra board space is needed outside of the small 0.1" headers. These are yet another type of crimp-and-poke connector that works well. You can buy a whole kit of these from Amazon for about $12.

Right angle or straight?

, and pin 1 (square pad) on the right side.



Note that if you use a right angle connector, the tab is on the top, which corresponds to the tab on the vertical header located away from the board edge. Ideally it uses a different footprint.

Cables and crimp tools

Tin or Gold?

Crimp-and-Poke or IDC?

Sorry, but there are still more choices. Both Amp and Molex make Crimp-and-poke connectors. But Amp also makes IDC connectors. Some people swear by the IDC types. You simply push the wire onto the back of the connector with a low cost tool called a T-Handle. No tiny pins to handle, no poking needed. However you will need to decide wire size and use only one wire size for all your connections. The color of the connector corresponds to its wire size.

With Crimp-and-poke, pins can be used with a range of wire sizes. I generally use 26AWG for signals, and 22AWG for power. One size pin can handle 26, 24, and 22AWG.