I absolutely loved Leiden, which is a beautiful university town and is a quick train ride from Haarlem. It is the home of Leiden University, which is one of the oldest universities in the country, and is quite lovely with charming cobblestone streets, 17th century gabled houses. It has many historic buildings but does not have the "touristy" feel of many other places. It's a much more livable feel. The city has many picturesque canals and waterways, which are lovely to walk along and there are boat tours you can take. And there are lots of parks, gardens, and green spaces in Leiden.
There are several museums, including the Rijksmuseum van Oudheden (National Museum of Antiquities), which has an wonderful collection of Egyptian artifacts. There is the Museum De Lakenhal (Municipal Museum), and the Naturalis Biodiversity Center. The Hortus Botanicus (botanical garden), which was established in 1590, was the site of the planting of Holland’s first tulip bulbs in 1593. Rembrandt was born in Leiden, as was Albert Einstein, who taught at Leiden University. St. Pieterskerk is quite historic and worth seeing, even if you just check out the outside of it. Rembrandt's parents were married and buried there.
In terms of transportation, Leiden has very easy access by train to other cities in the Netherlands. Its charm and beauty and overall residential atmosphere made it a wonderful destination. I hate to gush too much, but I really cannot recommend Leiden enough.
I did enjoy den Haag, but do not feel it compares to the charm of Leiden. I did not go to Delft.