The idea of developing your campaign through small, but ever-expanding, hex maps, was inspired by Greywulf's Six sided gaming: Hex magicarticle. With Greywulf's permission, I've expanded the concept a bit. Part 1 described how to size your beginning map and determine terrain. In this post, I'll provide some guidelines for populating your hexes with encounters and lay the groundwork for adventure.
The Hex Map
As a refresher, the hex map I started in the previous post is shown at right, though I've gone ahead and filled out the remaining terrain as outlined in Part 1. Please note the hex numbers shown, as I'll use them to identify the locations of the encounters.
As a reminder, each individual hex is 5 miles across; the large hex—called an atlas hex—is 25 miles across and matches the scale of the Atlas template (q.v., Hex Templates).
For our purposes, an encounter is any feature that has the potential to challenge the PCs or serve as the basis for adventure. There are two types of encounters:
Major - large or multi-layered encounters, often the focus of the region; for the PCs, interactions with these require careful thought and planning
Minor - small or fairly straight-forward encounters; these represent diversionary challenges for the PCs or opportunities to detail the campaign for the GM
For each atlas hex, there is a chance of a single major encounter and a variable number of minor encounters. The frequency of major and minor encounters varies according to the atlas hex's primary terrain type and climate, as shown below:
Major Encounter 
Minor Encounter 
Modifiers (apply to chance of Major encounters)
Roll once for each atlas hex
Roll this many d6's; each result of "1" indicates a minor encounter
When a major encounter is indicated, roll 1d6 to determine its identity. Place the encounter in any whole sub-hex within the atlas hex and note the hex number to record its location. Recall that there is never more than one major encounter in a single atlas hex. (UPDATE 8/26/15 - added links to the major encounters articles, which contain random tables with more detail than provided below.)
Settlement - a town or city that supports a significant population
Fortress - a large, fortified holding owned by a noble or self-styled lord, always with an armed garrison and (usually) a small population of civilians
Religious order - a temple, monastery, or non-secular fighting order (Alignment (d6): 1-2 Lawful, 3-5 Neutral, 6 Chaotic)
Ruin - the remains of an entire settlement or population complex, abandoned by original occupants because of (d6: 1 disease, 2-4 attack, or 5-6 migration)
Monster - the lair of a rare or very rare creature
Natural Phenomenon - an unusual natural feature (d6: 1 unseasonal or intense weather, 2-3 geothermal activity, 4-5 peculiar growth or blight, 6 oasis or grove)
Roll 1d20 on the following list for each minor encounter indicated. Distribute minor encounters throughout the hex as you see fit. As with major encounters, note the hex number of each to record its location.
Settlement - a village or hamlet with a small to moderate population
Fort - a small fortified holding owned by a noble, military leader, fighting order, or adventurer
Ruin - the remains of a single structure whose original purpose was (d6: 1-2 tomb, 3 holding, 4-5 other structure, 6 dwelling; 60% chance it's a shipwreck if located in a water hex)
Monster - the lair of a common or uncommon creature
Wandering Monster - creature type based on current habitat; creature is (d6: 1-2 establishing a lair, 3-5 scouting/foraging, 6 lost)
Camp, industrial - production facility for some natural resource, based on terrain (Water/fishery, Swamp/peat, Desert/oasis, Plains/farming/ranching, Forest/logging, Hills or Mountain/mining)
Camp, semi-permanent - a way-station for (d6: 1-2 trappers, 3-4 hunters, 5 drovers, 6 messengers)
Beacon - a long-range signalling/communication device (lighthouse if on/near water; 20% chance of being magical) operated by (d6: 1-2 guild, 3 local lord, 4-6 council of nearest settlement)
Construction Site - a structure is being erected here (d6: 1 fortification, 2-3 infrastructure, 4-5 homestead, 6 religious centre)
Battlefield - the site of a major battle (20% chance of containing salvageable gear; 10% chance that the area is haunted by the spirits of the slain)
Isolated - the dwelling of some outsider (d6: 1 hermit, 2 mad hermit, 3 oracle, 4 retired adventurer, 5 outlaw, 6 homestead; 40% chance dwelling is fortified)
Sacred Ground - a protected area, designated as a (d6: 1-3 burial grounds, 4-5 consecrated area, 6 hunting range)
Crossing - a bridge, ford, or pass (20% chance that it's in disrepair; if serviceable, 60% chance that a toll is charged)
Ancient Structure - a construction of antiquity (d6: 1-3 grave marker, 4 astrological construction, 5-6 pagan shrine; 10% chance that is possesses magical properties)
Special Hazard - an environmental danger exists here (d6: 1-2 poison, 3, disease, 4 unstable ground, 5 strong electromagnetic field, 6 radiation)
Treasure - a cache of valuables is rumoured to lie hidden here (40% chance of actually existing; 20% chance that it's unguarded, but certainly not easy to obtain)
Contested - the area is fought over by 2 or more factions because of (d6: 1-2 valuable resources, 3 abundant food, 4-5 strategic location, 6 religious significance)
Natural Resource - a valuable commodity is located here (d6: 1-2 rare herbs, 3-4 rare mineral (lodestone, quicksilver), 5 meteoric steel, 6 heavy water)
Supernatural Feature - an unexplained effect or object exists here (d6: 1-2 teleportation portal, 3 dimensional gate, 4 anti-magic field, 5-6 wild-magic field)
Gathering Place - a meeting place, relatively free from outside influence (d6: 1-3 tribal moot, 4-5 free trading post, 6 hospitaliers)
Once placed, encounters are yours to detail, based on the flavour of your campaign, the challenge you want to provide, the ability of the characters, and the game system you're playing. That said, there are two cardinal rules to placing encounters: First, encounters will co-mingle with other encounters in the same or nearby hexes. Nothing in your setting exists in a vacuum, so where possible (and sensible), populations will interact, cooperating with or opposing each other as resources and alignment dictate. Settlements will practice trade, monsters will prey on the weak, local people will know about local ruins, and adventuring spots will possess a history that intersects with other encounters. As you place encounters, then, be mindful of potential connections between them, and don't be shy about exploiting associations that fit well together.
Second, to extract maximum creativity, make it a policy to modify any encounter to suit the terrain, not the other way round. For example, a monastery located on the plains or in a forest might be fairly typical, but a monastery in the mountains might be occupied by highly private monks with a strange obsession with (or sinister reason for) seclusion. A swamp monastery might be populated by a sect of degenerate cenobites who worship a slimy, evil frog god, whereas a monastery in a water hex might be a old ship run aground, and the monks' mission is to keep eternal guard over whatever cargo is still in the hold. Be creative—almost any idea outside the norm becomes plausible if given some considered background.
Finally, there's an unwritten rule (which, oddly, I feel the need to write down): don't let the dice dictate your design. This exercise is designed to make campaign design easier, not foolproof. You still need to decide if what the dice are telling you makes sense. If they're not, use their results as suggestions and tweak what you need to tell the story you want.
To keep things quick, I'll determine encounters for just the single, central atlas hex on my map. The hex's primary terrain is "Plains," for a 60% chance of a major encounter and I roll 6d6 for minor encounters (because the map depicts a temperate zone (determined in Part 1), there is no climate adjustment). I roll 42 on the percentile die (for 1 major encounter) and let's say I come up 5 minor encounters:
Major encounter: Fortress [05.04] - Fort Torin, a keep ruled by Lord Dordi Nonahi (AL Lawful), and the attached village of Looma (pop. 344 + 18 in garrison)
Minor encounter: Isolated [04.06] - the outlaw, Usufo Hilden (AL Neutral), has a treehouse hideout, which he shares with 3 other bandits
Minor encounter: Contested [05.02] - Lord Nonahi's plan to revive an abandoned silver mine is contested by a local dwarf clan declaring that it cannot be reopened (but will not say why)
Minor encounter: Wandering Monster [03.03] - goblin patrols have been sighted here, more frequently in recent weeks; they represent scouting parties from a tribe in the next hex
Minor encounter: Gathering Place [07.03] - West Hailford, a walled trading post, is a safe haven for travellers; visitors of all sorts obey the local law forbidding violence within the post's walls
Minor encounter: Ancient Structure [06.06] - a stone table of pagan origin stands here; during the new moon, the moss that covers it gives off a shimmering verdant glow
I made some liberal interpretations of the results from the tables above, but that's the point—these are just idea-starters to get you thinking about who and what exist in the hex and, more importantly, how they might interact with each other.
You may wish to devise random encounter tables specific to your map, using whatever guidelines are pertinent to your game system and campaign. Include wandering monsters particular to the area (based on climate and terrain); patrols from nearby settlements, garrisons, or outposts; and events that may be related to certain encounters (e.g., a freak storm caused by a special hazard, supernatural feature, or natural phenomenon in a nearby hex). I suggest you create a single table for the entire map.
Rumours are also important, as they frequently serve as the basis for adventure hooks. Create a single table of tales and rumours for the entire map, obviously using the encounters you've placed, but also (more importantly) the connections between those encounters, as these are usually easier for you to fabricate and more tantalising to the PCs. You probably don't need to be reminded of this, but make sure you sprinkle a few false rumours in the mix, as well a few half-truths.
The end result of this exercise is a fledging campaign setting that will keep your players busy for some time. The format lends itself easily to the Busy GM's creed: Don't do more work than necessary. And, as a bonus, it's very simple to expand the campaign as you need to using the Hex Template system outlined elsewhere on this site.