For my Arcana Evolved/3.5 hybrid game, I use most of the rules presented by Fantasy Flight's "Sorcery and Steam", with the addition of the gunpowder critical fumble rule (or Malfunction Rating 1) given to firearms in the WarCraft d20 RPG. In the event of a natural one when handling any sort of gunpowder device, whether as an attack roll or even a skill check, the weapon malfunctions, (usually exploding in the user's hands for the same damage as the shot would do, DC 15 reflex for half). Also, firearms do not automatically pierce through armor and shields, and use normal attack rolls. Further, I treat them as a category of Exotic Weapons, requiring a feat to gain proficiency, which generally means that they're used by characters with a good dexterity, evasion and/or bonus feats to play with (Akashic, Unfettered, Rogue, etc.) I also added in the Munitions skill as a class skill for the 3 aforementioned classes to promote the use not only of firearms, but of gunpowder explosives, and for the benefits of high-DC skill checks to reload times.
Essentially, this means that a normal, everyday guy who picks up a gun is probably not going to be proficient in it's use, and has a good chance of blowing up, and will be abysmally slow to reload. As such, guns are seen as somewhat eccentric weapons that aren't practical yet for mass-combat, and much like all the best equipment, is the forte of Adventurers and Nobles who have the time to invest in being exceptionally good with an exotic weapon.
Despite all these drawbacks, adventurers can still become very good at gunslinging. For instance, a 6th level Rogue or Unfettered could easily be proficient, have a reasonable chance to avoid serious injury from mishaps due to their good reflex saves, and have the feats (Rapid Reload) and skills (Munitions DC 25) to load and fire a flintlock within a single round. Couple this with Quick Draw, and a liberal use of speedburst, and there's little reason that a character could not take his full iterative attacks with a pair of firearms, though he would probably still be down the next round to reload both weapons, or else only be able to reload and fire one. While this isn't exactly realistic, it does drive home the superhuman nature of heroes and villains in the campaign as opposed to normal people, and allows even flintlocks to be a valid weapon-of-choice for a properly built character rather than simply and opening gambit.
In my current campaign, the party's 12th-level Unfettered carries 13 firearms upon his person, 9 normal flintlocks (one is +1), 3 double barrelled ones (again, one of them is +1), an a double-barrelled flintlock rifle. The +1 weapons are heirlooms from his parents, worn at his sides, the musket slung over his shoulder, and the remainder concealed in his coat, which has numerous pockets allowing it to function as a Heward's Handy Haversack, and his vast storehouse of ammunition in his Bag of Holding. While he carries a variety of other weapons, scavenged from various foes, his guns are generally the first and best offense that he has, making him the second highest damage dealer in the party (After the Party's Giant Shark Totem Warrior, who's Greatsword + 30 STR and Reach makes him the equivalent of a Meat Grinder). However, the Gunslinger's reliance on his equipment is much heavier than any other character in the party, and carrying that much gunpowder makes him a liability in an AoE effect should his Reflex saves fail despite his Evasion, and moreover, he often finds himself resorting to melee combat against foes with damage reduction greater than /+1 or magic, since he went for quantity over quality.
On another note, my campaign has also included a gunslinging NPC who was a Runethane, having adapted the Lock 'n Load spell from the pdf linked to by helpful people above into a Lesser Rune which he always kept inscribed on his personal flintlock. With their affinity for technology and "lawful" concepts, the Runethane actually works exceptionally well in a world that is attempting to modernize, as new runes are created to represent new aspects of the world (like guns and steam engines) and old runes are put to new uses (i.e. the rune of accuracy
Robert "Guns Don't Kill People...PC's do" Ranting
