I am looking for an alternative for the usual female header pins, one that has a lower profile than the traditional 8.3mm/0.33in high female header pins.
Adafruit has a low profile Female headers but when attached with the tradional male heade pins it still stands tall.
It doesnt have to be a through hole component, I found one that i really like but i am failing to search its name. 
It from the raspberry pi POE HAT, a good thing about this (for my case at least) is it can be set on the other side of the board thus lowering the profile even more
but if there are others please do tell
Best Answer
There are 'strips' you can get with individual sockets. Types I could find with a quick search looks like this:
…or…
You can also embed holes into your PCB as described in another answer:
Hard to get any lower than that.