Practicality and convenience is why I went for 5 doors over 3 - can't really think of any other reasons! Though my daughter is long past needing a child seat in the back, it's still a pain when ferrying more than two passengers about if you only have 3 doors. It's also nice to just be able to open a door to throw some shopping or a bag in the back. A major plus in favour of the Golf is that it is one of very few cars that still looks really good in 5 door guise.
Admittedly 3 doors looks a bit better, and saves you some cash, but for an everyday car I'll take 5 doors every day.