They SHOULD be a main thread for a certain topic that's likely to result in lots of threads, on account of either it's popularity or the wide-range of subtopics within that topic, and is ideally going to continue to be in use for some time.
They work best in the Games section, generally, where you have examples like the
Pokemon VG Megathread. This is a good example for a topic (Pokemon Video Games) that could do with being collaborated into one location. Since there are so many different Pokemon games, spin-offs and Anime (which is sometimes, but not always discussed), it makes sense to have one big topic gathering it all together.
Otherwise we might have 30 different Pokemon Topics. And each of those would be on a single specific Pokemon game, and chances are that they would be discussed for a while, but eventually fall into disuse when a new game comes out.
But in the Megathread it doesn't matter if people stop posting about, say, Pokemon X/Y because OR/AS has come out, because people discussing OR/AS will still be discussing it in the same place.
And in addition to that, if I want to go and find out what advice or discussion people had for say, Pokemon Diamond/Pearl, then I can go straight to that topic, which likely isn't going to be too far from the front page.
If there was just a single Pokemon Diamond/Pearl topic that stopped being used 4 years ago, then I'd have to go searching for it, and if there were multiple topics I'd have to scour all of them for the info I want.
Unfortunately though, there's no actual rule or policing on what is or isn't a megathread.
Hence there are some topics named "Megathread", despite them being a really specific or even short-lived thing.
And even if there is a Megathread, there's nothing saying you can't make a new topic about the same thing. The only 'punishment' for doing that is the communities reaction to you making a second topic.
