For many students and employees who move to the Netherlands, finding housing can be a serious challenge. Housing was something that kept me awake at night during my first months in Delft. The key to finding a suitable place to live, is just giving yourself enough time to look around.
If you are coming to the Netherlands by yourself, I advise you to look for a temporary place where you can stay a few weeks first. From there, you can visit other places and look for a room or house that suits your fancy. Don't book housing for an entire year from abroad - you always get disappointed.
The following websites can help you finding temporary housing:
Otherwise, you can stay in a hostel, bed and breakfast, hotel or camping site for a few days while trying to secure your spot.
If you are coming to the Netherlands with your family, it might be better to apply for university housing. University housing typically gives you a place to live for the first year, while you accommodate your family in the country. Many universities cooperate with Duwo - and there are good and bad stories about university housing. The major advantage of renting through a centralized housing agency is the security that you will have a place when you arrive - something that I consider a big *must* for families. The disadvantage, however, is that they tend to charge a lot of extra application and administration fees.
When it comes to finding your place for the next few years, you might get scared off at first. Some housing is very expensive in the Netherlands - there is a shortage of student rooms. There is public housing, provided by for example Woonnet Haaglanden, but the waiting lists are very long: at least 3 years of waiting time. If you are coming for a PhD program of 4 years, then your chances of finally getting public housing are rather small. Private housing companies, such as RotsVast and Van der Vorm (from whom I rented - but their administration is a massive mess), fill the void in the housing market and offer apartments for rent - at prices higher than the public sector.
When you want to live in a room in a shared house, you often have to go to an "instemming"(literally translated: "voting in"). Sometimes that means that 100 students vying for one room are gathered in a house, get to introduce themselves in one sentence, and then the residents of the house randomly point at a number of faces they like, to further interview these folks. You might take your chances at such an event, but I must say that I never got to the second round.
Moreover, an "instemming" is typical for Bachelor's and Master's students. As a PhD student in the Netherlands, you are an employee of the university, and you're typically expected to show up to your office early in the morning. The "student life" thing just might not fit you anymore...
If you want to cut costs, I recommend you looking for a shared house/apartment. Many PhD students in the Netherlands live in shared accommodation. A good website to look for a room for rent or prospective roommates (when you decide to take a contract and look for peers to share costs) is Kamernet. Also, when you move to the Netherlands by yourself, it can be nice to be in a shared house, so that you can make friends and ask for advice from senior PhD students, who might have had to do all the paperwork that you are about to embark upon.
The best advice that I can give you, is to let all your colleagues know upfront that you are looking for housing.
I found my first room in Delft because a schoolmate from high school told a friend in Delft that I was going there too, and his roommate happened to be away for a semester to study abroad - that was the sublet from where I could get started on finding a place. I then found my home in Delft because my colleague knew a PhD student who was finishing and he asked her if her room would be available. I ended up taking over her room, and buying all her furniture.