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HAve a few pots of herbs which we keep on kitchin windowsill (although do put them out on the patio once in a while) Noticed that every time we water them lots of small flies are disturbed from the soil and start to flie around.
Anyway to remove these flies (pref an organic method)

Thanks.

Spooky,
sounds like some sort of aphid to me, which have possibly overwintered in the relative warmth & humidity of your kitchen. 
Best bet is probably to keep them outdoors as much as possible and put up a big sign saying "hoverflies and ladybirds supersized here" ;D; if your beneficial insects can't read, put the herbs near something that attracts lots of hoverflies.  If they are aphids they will concentrate on the fresh growth and you could wash them off by gently wiping the undersides of the leaves with soapy water.
You don't mention what herbs they are - many of them respond well to cutting back to about a third of their size and re-potting (at which point you can wash the roots bare and clear all infestation that way).  This is what we did with our mint and sage this spring.

Or could they be something like little fruit flies that live in the compost?  I get them sometimes in my conservatory pots.

Found this about them....

http://www.the-piedpiper.co.uk/th6h.htm

Sounds like Sciarid flies to me,their maggots eat the roots of plants :( google and you will find sites on how to get rid of it, hope this helps /shades x

thanks for the replies. will repot them this week and get some grit/gravel to cover the soil up with. hopefully that will sort it out.