Do windows on the side of the fuselage increase drag?
The long length of an airliner fuselage ensures turbulent flow at the station of the cabin windows, so their only contribution to friction drag are the gaps between metal and polycarbonate. The transition from a laminar to a turbulent boundary layer happens before the windows start. In Sighard Hoerner's classic Fluid Dynamic Drag we find in Chapter V these figures on the drag of surface imperfections:



The size of the gaps and the dynamic pressure at their location drives their drag contribution. Let's assume the windows are 0.4&nbsp;m high, the grooves 2.5&nbsp;mm (0.1") wide and shallow enough to have a drag coefficient of 0.008. Let's further assume we talk of a Boeing 747-200 with 100 such windows per side and restrict the drag calculation to the crossflow over the vertical part of the gaps. The full opening area of all gaps is $2\cdot100\cdot2\cdot0.4\cdot0.0025$ = 0.4&nbsp;m² or 0.078% of the reference area of the 747. Wikipedia gives the parasitic drag coefficient of the Boeing 747 as 0.022, so the windows contribute one threethousandfivehundreth of that drag. Negligible, in other words.

But there is another source of drag: The windows are heavier than the metal which they replace, and to carry them around will increase induced drag. If we again assume 200 windows for a Boeing 747-200 at 7 kg each (these are from pre-polycarbonate times!), they weigh a total of 1.4 tons. This is 0.8% of its empty mass and equivalent to 12-14 passengers. To find the impact of this mass on a long-range flight over 6000 NM, we can use the Breguet equation; once with and once without the 1.4&nbsp;tons of additional mass. The empty mass of the Boeing 747-200 plus 50&nbsp;tons of payload is 228,100&nbsp;kg, its L/D is 16, the specific fuel burn of its JT-9D-7 engines is $b_f$ = 0.0000184&nbsp;kg/Ns and the cruise speed is Mach&nbsp;0.84, which equates to $v$ = 250&nbsp;m/s in FL 350:

$$m_1 = m_2\cdot e^{\frac{R\cdot g\cdot b_f}{v\cdot L/D}}$$

When we use $R$&nbsp;=&nbsp;11,112 km and run this once with landing masses $m_2$&nbsp;=&nbsp;228,100 kg and again with $m_2$&nbsp;=&nbsp;226,700 kg, the difference in $m_1$ is bigger by a factor of 1.65 (the take-off masses $m_1$ are 376,584&nbsp;kg with and 374,237&nbsp;kg without windows), so carrying the windows around costs the Boeing 747-200 911&nbsp;kg of fuel or 0.61% of the total fuel mass per flight. This is one onehundredsixtythird of the total drag - still not much, but fourty times as much as the absolute contribution of the windows to friction drag (if we assume that the 747 flies at the polar point for optimum range).

This explains why conversions of airliners to freighters almost always replace the windows by metal plates but don't care that much about the gaps they leave. In the case of the 747 pictured below they are certainly big enough to be visible from afar.



A Japan Airlines Boeing 747 passenger-to-freighter conversion featuring aluminum window plugs. (Photo credit: Flickr)