First of all, let's clear up a fundamental misunderstanding: Marchetti's Constant does not state that a city's size is limited to one hour of commuting, but rather that people will adjust their routines such that they spend, on average, one hour commuting. This means it does not impose any restrictions on city size, it only supposes that people will live up to ~30 minutes from where they work (giving an average daily commute of 1 hour). In fact that's evident today already, where numerous cities take much more than an hour to commute from one side to the other (especially if you catch traffic at the wrong time!), though on average people live much closer than "the other side of the city" from where they work.
It does have implications on urban planning, though, such as implying that a residential zone without much work available in a 30-minute commute probably won't be much lived-in.
That said, the Supercities of the future are still likely to have very interesting modes of transport for when people do want to travel further than 30 minutes, and even for extending how far 30 minutes actually gets you:
Trains and Flying Cars
AndyD273 has already addressed these in his excellent answer. I'd just point out that China's 2010 1000kph train is no doubt slower than the express trains of the future, especially if vacuum tube trains become a reality. I'd also add that flying cars, barring some sort of hand-wavium that (at least partly) negates gravity, would necessarily be much more energy-intensive than surface-driving cars, meaning they'd never fully replace the latter.
The expressways of today are pretty much just wide boulevards with limited traffic lights so that you can drive from Point A to Point B more quickly. We're already on the cusp of the next generation, though: Expressways designed expressly for self-driving cars.
This would work in a way that blends high-speed trains with taxis: You would hail a car, get in, and it would take you to where you need to go. No having to bother with all that lane and signaling nonsense, either; advanced computer algorithms would dynamically adjust the paths of each individual car (in much the same way that air traffic controllers guide airplanes) so that each one has a clear path from Point A to Point B.
With expressways closed to any other vehicles, these computer-guided cars would be free to run just as fast as we can make their engines capable of, without fear of collisions; while unlikely to beat a high-speed train in a speed challenge, they would have an extraordinary advantage: There'd be no need to get out and transfer to a local leg, because your self-driving car could simply get off the expressway and -- albeit at a slower speed -- navigate surface streets to bring you directly to your destination! [NB: You'd probably put opaque windows in these things, at least while on the expressways, because your human passengers would very likely find themselves in a heightened state of anxiety if they can see the seemingly-chaotic mass of cars driving at high speeds through laneless roads, weaving between one another as they approach at deadly speeds head-on before veering off -- very often the most expedient path is not what we're used to seeing with our static concepts of "lanes" as "safe passing zones"!]
You could even physically separate the self-driving cars from everyone else by having them suspended underneath the expressways (a la the Total Recall reboot), freeing the surface to be available for manually-operated cars (if those even still exist...) or even high-speed trains.
This is already a thing today; I spent 6 years working from the office in my home for a company that would have otherwise required an 8-hour flight one way to get to their offices. That was your run-of-the-mill telecommuting though, where I'd be typing on my computer or talking on the phone all day; these days you can get yourself telepresence robots (link is just one example) to have a physical, mobile presence in an office on the other side of the globe, let alone one merely 800 km on the other side of the Supercity.
As these become more ubiquitous in office environments, commuting will become a lot less of a consideration.
In a very similar vein, MMO games have given us another option: The virtual office. After all, if you can get 25-50 people together for 8 hours to battle a pixelated dragon, certainly you could hold a 1-hour staff meeting in a similar manner? The advantage this has is that you can base your avatar on your own appearance, allowing others to still connect with you visually, and/or customize your avatar to your personal preferences (similar to the MMORPG character generators today), which has many of the same benefits (assuming you don't frequently change your appearance, that is). As VR systems improve, this is likely to become even more prevalent and more accepted.
After all, even today there's really no need for countless individuals to ever set foot in an office; as this becomes a more widely-accepted fact, and the various telepresence technologies provide comfort to the clingers-on of the "old ways", commuting will become more and more an artifact of a bygone era.