Our 2 year old golden retreiver has been coughing occasionally for the last couple of days as if she has something in her throat. It seems it happens when she is running around or laying on the floor for a while. Although she is able to bark and drink without any problems, I have looked down her throat but cant see anything down there. She coughs a bit and then seems to try to throw up but nothing comes up or if it does she swallows it back down before it comes out.She is currently on a course of anti-biotics for a urinary infection but she has been on these for over a week now. Any ideas what it could be?

There are several possibilities, but your vet is the best to diagnose any medical problem. I'd recommend you make an appointment for a consultation.
:)

I have made an appointment for saturday, I have been reading a bit on this site and it seems as though it might be kennel cough although we dont seem to get any phlegm. Some people say to flick the throat, is this a good idea?

The most likely cause is Kennel cough a highly contqageous condition like a cold or flu.  when you go to the Vet mention this as a possibility and do not go into the waiting room (it can be serious condition for the very old or young) with yoru dog, ask the vet to come out and see her.

Sounds like Kennel Cough to me, keep her away from all dogs until she has been seen by a vet.

It does sound like Kennel Cough, you could give a little paediatric Benilyn while you are waiting to see the vet, it doesn't cure Kennel Cough, nothing can, but it does ease their discomfort.
Can you not get an appointment before Saturday?  On the outside chance there is something stuck, that is rather a long time to leave it and must increase the risk of it causing a infection or abscess I feel.

i agree with the rest of the suggestions of kennel cough. As isabel said, theres no cure for kennel cough, and the kiddies benylin does work-my vet recommended using that when my girl had it. My vet suggested reducing the active exercise a little to minimise irritating the airways with panting.

nic