The best thing I ever did for my big-ass hexcrawls was establish what I call “encounter chains.” This is a series of escalating encounters with the same faction or NPC.
For example, a roving band of orc cultists cutting off people’s left hands. (I can’t take credit for this idea, it’s a riff on this.) The first encounter in this chain actually isn’t the orcs at all, but the result of one of their attacks–an upturned cart and a family of five (man, woman, three children), with the father’s left hand cut off and taken by the orcs. This is a fantastic non-combat encounter that lets you drop info about the orc cult and lets the players figure out all sorts of stuff–turn the cart back over, collect their scattered remaining supplies, offer some of their own, calm down the children, potentially healing magic on the father to at least stop the bleeding and cauterize the wound. Great stuff.
Then, the next time they find the orcs attempting to knock over another cart. This time the players can stop it. Whether any survive or not, the orcs will be aware that some group of assholes is going around cutting up their cult members, leading to the next encounter where the orcs have definitely set up an ambush for the players.
Eventually, of course, this all has to lead back to the players asking an orc who they’re with, where they live, what their goal is, and now there’s an orc lair on the map somewhere and the players will be figuring out how to lay siege on it.
Now, do this for three or four other things. For example: A guy who keeps ending up in mischievous trouble. Buried up to his neck in the middle of the road, enchanted by a satyr and strung up in a tree, stuck in a barrel in the river. Eventually this guy could be revealed to be a powerful NPC ally in disguise as a schmuck to throw people off his scent; a spy from a powerful organization, sent to deal with the same problems the PCs are dealing with (such as our orc cult).
Other simple examples: A group of roving barbarians, trying to summon a thunder goddess to cleanse the land. A migrating group of treants. An old man, with one eye, attended to by seven canaries, who turns out to be Bahamut, or Odin. A hungry dragon driven from its lair by evil adventurers. Etc. Be creative. Use whatever stuff you like. You can even pull the plotlines and factions from your favourite modules and drop them in, creating the powder keg effect (article forthcoming).
Once you have three or four of these encounter chains set up, scatter them on your table amongst other, single-service encounters–some just straight up combat (there’s a bulette! attack/run!), some avoidable (an Ettin is in a field looking for easy hunting prey), some unrelated people (like merchants or lost travellers).
Keeping an even keel between “random bullshit” and “ongoing plot threads” means the game never feels stale, and the players are never overwhelmed by too many threads to keep track of. I don’t recommend any more than four encounter chains at once; any more than that and the players could start to get overwhelmed by ongoing plot threads. It also helps if each encounter chain has a different amount of encounters in them–one chain that can be “solved” in three encounters, one that’s six or seven, one that’s about four. You can alter this based on the vibe of your table and campaign; if you had an encounter chain with five or six encounters and the players are clearly beginning to get annoyed, just jump to the end.
One thing to keep in mind is that you don’t have to develop every encounter in the chain at the beginning of your prep. You just need the first encounter. Once the players hit upon it, cross it off the encounter list and repopulate it with the next encounter between sessions. Easy money. You can also take any random encounter you’ve used and then decide after the fact to expand on it; maybe you introduce a merchant NPC and play him a little weirdly, and the players are interested and start speculating. Great opportunity to take that guy and turn him into an encounter chain!
