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I have three house keys and always hold them in my hand, always have done. Bit awkward now as the strap on my running watch is broken too though...so I have to hold that in the other hand!
I normally keep my keys in the pocket of my jacket - this normally works well - up to Saturday past when I lost said keys when they must have fallen out of my pocket when I went to check my *gasp* ipod....
I use a couple of methods. SIS marathon belt with the keys wrapped in kitchen roll. Put them in a small MP3 holder strapped to my arm. In a zipped pocket in my running tights.In winter in side a pair of running gloves.
Alternatively I just hope that the family will let me back in the house when I get back from a run and leave the keys at home.
Normally just hide the keys if I haven't got my MP3/phone bumbag with me, but if I have to take a key then in the small key pocket in my shorts, with the drawstring tied through the ring as belt and braces back up.
For races I leave the house keys in the car, and have a hair band looped through a hole on the car-key fob. I wrap the car fob in clingfilm (especially if raining, so it still works at the end!) and then put this in the key pocket, with the drawstring tied through the hair band - also helps keep it out the way and stops it bouncing around.
I always take just the one key and tie it to the strings of my shorts and tuck it in! It never comes off or stabs me in the leg.
I always wear shorts or training tights with either a zipped pocket or key pouch. Unfortunately, the pouch in one pair of shorts that I wear for races is a bit on the small side and last year, in a race, put my house keys and car key in there. One of my house keys pierced the central locking button on my car key, thus rendering it knackered.
Single key - largeish safety pin through the key then pinned to waistband of my shorts.
Large or multiple keys - largeish safety pin through the keyring then pinned to the waistband of my shorts but on the inside (on the right hip usually). As I wear lycra shorts this stops them jangling about and they stay where they're put.