About ten minutes walk with a suitcase on wheels from the railway station and you're faced with Leiden's wonderful Rapenburg. The first building on the left side of the canal is the magnificent De Doelen Hotel. I spent a wonderful week there and via a German film company, discovered, in 1910, it was the meeting place for Sigmund Freud and Gustav Mahler. This is a very old building. It creaks, is oddly-shaped and not suitable for those who like anonymous square boxes or rooms that are identical. But if, like me, you want a place of character then it's ideal.
It's situated right in the heart of the ancient city and nearby there are numerous first class restaurants and coffee houses. Just across the canal and up the Rapenburg you can spend a lot of time in the Hortus Botannicus or venture a bit further and stand on the spot where the Pilgrim Fathers embarked on their journey to America.
I found the staff very helpful and welcoming and the breakfast suited my tastes.

best breakfasts we had in the Netherlands. Beautiful hotel, very nice people, great location.

the more expensive rooms are probably worth the few extra euros.

This old canal house in Leiden has a great central location, but which is a bit of a walk from the train station. There is no elevator, and the 2nd and 3rd floors can only be reached by a very steep staircase. Rooms on the top floor are quite small, as are the bathrooms, but adequate for a home base if you don't plan to stay in the room much. The breakfast is very poor -- if the cost is not included in your quote for a room, I'd suggest you walk down the street a bit to one of the restaurants for a more substantial meal. For convenience, the Tulip Inn and Golden Tulip hotels are just adjacent to the train station and more modern. The Holiday Inn is very modern and has air conditioning -- but is very distant from the city center.

Bearing in mind that Leiden just isn't the town for great hotels, I would definitely recommend to stay here. Most of the larger hotels are outside the city centre. And I found that The Doelen is quite a bit better than Nieuw Minerva, the other mid-size/mid-price hotel in the centre, both in terms of location and service. It is true that their rooms vary in size and quality, but the staff was entirely candid about that when I booked and they helped me to choose the right room for that particular stay. Also, the staff was very flexible and helpful when faced with my - sometimes burdensome - requests.