I've really enjoyed reading through Sine Nomine Publishing's An Echo Resounding: Lordship and War in Untamed Lands by Kevin Crawford. Like Red Tide before it, there's a ton of great sandbox advice. One of my favorite concepts, simply due to its sheer simplicity, is the concept of the Hall of Infamy. Briefly, the "Hall of Infamy" is a simple process of creating a short, manageable list of major villains that will help shape regional events over the course of a campaign. These villains aren't instruments of railroading; instead, these could be considered background material that becomes powerful NPCs who could be enemies, rivals, or more rarely contacts or even allies. These are the forces behind the more powerful changes that take place in the setting over time.
To build a Hall of Infamy, you will identify seven bad guys. You start at the top with the Supreme Bad Guy of the setting, then you choose two "Name" level Bad Guys. Finally, you choose four Significant "mid-level" villains. These constitute your regional Hall of Infamy. All other lairs and villains are likely local affairs, so you don't have to worry about why the PCs haven't heard about them from their early years of adventuring. (And if seven regional villains aren't enough for you, you can always repeat the exercise again and you'll have fourteen to work with.)
For the Isles of the Saharan Sea, I thought I'd create a "Hall of Infamy," just to explore the concept and see how it works out for me. First, I started with the Supreme Bad Guy:
Mavarasha, Light Upon the Throne Triumphant
The Vanaran known as Mavarasha, Light Upon the Throne Triumphant, is a devoted priest of Thanatos, the Flame Lord. Conquest is a sacred responsibility to Thanatos, and the Light Upon the Throne Triumphant is no stranger to war and battle. He has conquered many of the Smoking Isles, and has set his sights on the islands closer to the mainland of Mediterranea. Mavarasha wears the Flamegold Warmask into battle, whether on land or see, as a sign of his devotion to the Flame Lord.
As you can see, I chose to follow a mystical path for the Supreme Bad Guy, and a priest of a war god seemed like a nice change of pace from a necromancer or a diabolist. Continuing on, I decided to create two "name" level Bad Guys, one based on a powerful warrior and the other on a powerful rogue.
Peleon Nightshade, Expatriated Grandmaster of the Brotherhood of the Black Rose
Master Peleon was once the Grandmaster of the Brotherhood of the Black Rose, a specially trained group of spies and mercenaries specialized in espionage, sabotage, infiltration and assassination (aka ninjas). He is a master of the unorthodox warfare and unarmed combat techniques employed by the Black Rose (i.e. ninja master). When internal strife led to the eviction of Master Peleon and his loyal followers from the Brotherhood, the former Grandmaster set up shop elsewhere and is now using his band's talents to infiltrate and manipulate foreign courts, seizing political control without direct confrontation. Because of the techniques used, attacks by Master Peleon's Black Rose Rogues are often blamed on the Black Rose proper. This is causing considerable friction between the Brotherhood and some of their clients, much to Master Peleon's personal delight.
Warlord Tal-kash, Zegoth General
When the serpentfolk mysteriously disappeared without warning or reason, many servitors of the "master race" panicked. One of the more competent and knowledgeable tacticians among the gorilla-men, Warlord Tal-kash quickly seized the opportunity to gain control of the zegoth warriors under his command. With an army and an armada under his command, Warlord Tal-kash has established a small empire from which he sends his demands for tribute from nearby islands. When someone stands up to the zegoth general, he raids and harangues his foes until he has conquered them and thus brought new subject lands under his control.
Tomorrow, I'll complete my "Hall of Infamy" with four significant "mid-level" regional villains. These should include a society of evil sword-mages, a Tarthani pirate Commodore, and two other interesting foes.