Well I don't think there are hard and fast rules because Sales Tax and Service charge are normally added to your bill.
In the Hotel's the staff get a share of the service charge.
In cafes and restaurants outside Hotel's check your bill and if the service charge is included, it is very much up to you whether you leave an extra tip. If the service really has been good, 5% is quite acceptable. If you are only ordering a coffee/tea/cold drink from a pavement cafe either 1 or 2 LE is enough.
I am not being mean here, but most places the tips are pooled with everyone getting a share, which i think is a pity as some waiters are better than others.