1. He's stuck to a genre that, while still quite popular, does not require an enormous development team. The place for gaming startups is not in the business of the "big players", but working on games whose main attraction is creative content and enjoyable gameplay, not high-end graphics and enormous amounts of hand-crafted content. Because of this, ZUN can develop roughly one game a year for the most popular amateur (doujin) game series in Japan in his spare time... and still have time to work full-time at Taito corporation! See Braid for another example of a relatively low-budget game that made it big.

2. The primary attraction of his games is probably the incredibly well-made musical scores: each game has a full soundtrack, with tracks for every level and boss fight. This serves as a "grab": the easiest way to get someone's attention is a case of "that looks cool" or "that sounds cool." His games certainly do the latter. If you can get a talented artist, music is not something that inherently takes a great deal of time to produce, unlike enormous amounts of 3D modeling or other forms of content. Most importantly, people simply like listening to good music while playing a game: if you find people are turning off the music to play their own during a game, you have done it wrong.

3. In the end, remember that enormous resources and marketing are not necessary to create a game. ZUN has certainly proven this true: he has gone from making hobby games in college to being the sole developer of a game series so popular that the fanbase has its own concert, its own convention so large it rents out the Tokyo Big Sight convention center, and makes up almost 5% of Comiket. Yet he never did any significant marketing--his fans marketed the game for him. And he still outright refuses to sign any rights over to a major corporation for any sort of higher-budget game or non-game adaptation.

Now, perhaps ZUN was lucky. Or perhaps in one of his drunken moments (he's notorious for his love of beer), he struck a goldmine of brilliance that allowed him to become so successful. But he's certainly not unique: the way to success for a small games developer is to make niche games and acquire a dedicated fanbase, not to aim at the Halo market.

When speaking of console gaming there is a considerably larger amount of formality and regulation than most web startups because of the influence manufacturers and publishers have. You work on their hardware, you are funded by hitting their milestone definitions, you are beholden to their marketing plans, and you cannot get distribution without their approvals. Studios that do big AAA titles are perpetually one project away from bankruptcy because big games ramp up to a huge staff for full production(which ideally occurs once the major unknowns of the gameplay, prototypes, engine, tools, pipeline etc. have been worked out) and unless they have a new project waiting once the first one ships, they're burning through massive overhead and face firing half or more of their employees or shutting down. The place I work for specifically avoids taking on big projects because of crushing past experiences.

Independents face a problem more similar to the early-stage startup of getting traction in the marketplace. They typically succeed via radical product differentiation, since the other angle(high quality) is covered by console developers already. This market has diverged into many subsets - to name the major ones: downloadable games, browser-based multiplayer, Flash games... each one has different production requirements and monetization strategies. While you can find plenty of success stories....there are also plenty of starving indies out there. As well, indies (as a rule) are less likely to make their games available as an ongoing, continuously improved service in the way a web company does. But the ones that go the service route, in my eyes, are more likely to succeed long-term than those following a "shipped product" model. To succeed as an indie you really need a rabid fanbase that follows your brand; the alternative is to jump onto the bandwagon of the week(casual games, girl games, etc.) and peddle your clone against 10000 other clones, which ultimately leads to a quality war and the console market situation.

Finally.....the biggest difference between websites and games is collision detection. To put it the way my boss does, "collision is gameplay." Not all games need collision, but those which involve simulated physical interactions do, and that requirement comes up astoundingly often, so it's a cornerstone game programming task. Plus, the particular implementation of collision radically influences the game so it's not a matter of dropping in library code.

That's not to say that the programming's the only problem - art is a problem because it always takes a long time, and game design is an unbounded-size problem. Solid game design happens after prototyping many different gameplay mechanics in isolation, keeping the ones that work, and then iterating over their integration until a satisfactory combination is achieved. This means: do a lot of work. Throw most of the work out. The leftover crumbs ship.

An ambitious project I am taking on now in my spare time is the angle of simplifying the game development process itself, with a website that promotes sharing and reuse of game-related content under Creative Commons. Long-term I want to add editing tools to create specific game types, but that is an easy task to underestimate and the web entrepreneurs that I've seen take it on so far have either grossly cut back on the features to get something done in a few weeks(making the service mostly useless) or allowed the scope to grow too large, finally failing after a depressingly massive effort. (see Gameclay)