A highway goes directly through the Gate Tower Building in Osaka, Japan; a monorail line goes directly through an apartment block in Chongqing, China.
It’s difficult to build new transportation routes in any dense urban area. The amount of land you need to purchase or requisition can make development prohibitively expensive. If you can acquire the land at all! Depending on local laws, it may take just one hold-out landholder to ruin a whole project. So, in a couple of places, architects and urban planners have come up with a rather novel solution: why can’t we all just get along?
The Ikeda Route of the Hanshin Expressway in Osaka, Japan, has an off-ramp that goes directly through a building. The Gate Tower Building is the result of a compromise between the city and the landowners: you let us construct an office building here, and we’ll leave a big hole for the motorway. Incredibly, the two constructions do not touch, and a large amount of sound-proofing protects the inhabitants from the worst of the traffic noise.
Line Two of the Chongqing Rail Transit system in Chongqing, China, was one of the country’s first monorails. It is famously quiet. This is a good thing, because it passes directly through an apartment block. There’s even a stop (Liziba Station) inside the building – which must be very convenient.
I have yet to find any buildings pierced by runways or canals. (Although there is a pub in Nottingham, UK, that has a working canal running into it, the canal doesn’t come out the other side. And aircraft runways like to run across roads and railway tracks rather than through buildings.)