Human have begun colonizing the solar system using the ablative laser microwave drive, our next target is Proxima Centauri and inbetween there is basically nothing except dust and occasional asteroids which is entirely avoidable even with blindfold. What can be the reason to install plain windows onboard when almost every spacecraft is running on autopilot? The journey might span several decades... as usual no FTL nor cryogenic freezing etc you get the drift.
If there's no FTL or cryogenics involved, there's going to be real people living on these ships. Most people don't deal well with feelings of claustrophobia; they're going to want to see outside every so often. Windows are a cheap and effective way of doing that; unless I'm mistaken, the ISS and the space shuttles all have windows to some degree. Seriously, the mental health of passengers and crew is something really important to consider; you don't want the guy repairing a leak to be badly sleep-deprived or paranoid as the result of such concerns.
Windows can also make for one form of failsafe in the event of sensor failure. Granted, if you actually have to rely on visual contact to navigate you're probably doomed already, but having an open observation deck with a few telescopes would be a good idea (as long as it's possible to seal it off from the rest of the ship in the event of a serious breach).
If you want more details, take a look at my answer to this question, which is concerned with the practicality of having exposed bridges (bridges with windows) on combat vessels. It would also be worthwhile to look at the other answers there.
There is no compelling reason to have many windows in an interplanetary space ship. Windows add weight, complexity and possible points of failure, and should be avoided as much as possible.
However, there have been times where windows have proved useful for monitoring the vessel itself. Apollo 13 noticed the venting of some gas into space, providing a major clue as to what had happened and the seriousness of the event. They used reports of the position of the venting gas to help determine what it was that was leaking (they also used the thrust effects from this gas on the vehicles attitude to estimate the source).
On the ISS, commander Chris Hadfield noticed through a window that flakes of something were departing from the station. This turned out to be an ammonia coolant leak.
It can be assumed that astronauts on your vessel will need to make periodic spacewalks, to perform maintenance. It may be worth the cost of the window to be able to observe them directly from inside.
It's arguable that video cameras would provide most of the above functionality. For stellar navigation, and monitoring of the destination as it approaches, telescopes penetrating or mounted on the outside of the hull would suffice, but a window or two would provide a nice backup.
Humans, being humans, probably want a few windows to look out of, just to look out of. Psychology onboard a very long endurance mission is very important, and will in some cases override pure engineering arguments. One observatory, and a few strategically placed portholes would probably be acceptable.
People have mentioned passengers wanting to see out and the useful ability to be able to quickly see if there's anything wrong with the outside of the ship, but we're forgetting something vital here - navigation.
Sure, you're in space and there's going to be a fancy computer doing all the legwork, but in the event of a failure you need a last resort option. Even today, ships at sea should have a compass and someone who knows how to use a sextant. You can actually use similar methods to navigate in space, Michael Collins had a sextant on board Gemini 10 for this very reason (although due to atmospheric conditions it was ineffective). There's also Apollo 13, where Jim Lovell controlled an acceleration burn simply by lining up the Earth and the Sun in his window.
There would be no worse fate than suffering a navigation systems failure and knowing that you had the expertise on board to get from A to B, but without any way of looking outside.