You've got three main approaches to consider, and a combination might be your best bet.
 

If you are in a multi-horse situation, such as a boarding or breeding farm, you must convince the other horse owners to join you in your efforts however, as merely making one set of manure piles egg-free won't help much. For the best results, have the entire horse population begin the treatment, early in the season, and keep it up during the warm months until the flies have died off with the frost.

For an old-time method that many owners still swear by, feed vinegar on a daily basis. You'd be surprised, horses will take up to a cup of the sour stuff in their grain, after a little introduction, and in theory it makes their skin less palatable. Since horses taste flavors differently than people, don't worry that their feed bins smell like a salad bar -- just be sure you're using apple cider vinegar, and that they're cleaning up their daily meals.

With the chemical applications, there's something else to keep in mind. Different fly pests arrive at varied parts of the summer/fall season, so what works on one thing (gnats, shad flies, etc.) may not be effective later in the season or at a different time of day. Test your products, and keep watching to see what's working and when.

 If chemicals don't please you or your horse, or they're not enough, a number of fly sheets, fly masks, and fly leg wraps have come on the market. Don't ask how you're supposed to get them on the flies, it's a secret.

For most horse owners, the wrap-around masks are a blessing, as they protect delicate eyes from fly attacks, as well as offering some shielding from the sun. Add-on ear covers can be had too, although some of them are rather difficult to keep on if the horse finds them an annoyance.

 The fly sheets work well, by most reports, although in hot, muggy areas the animals may feel an increase in the heat under that layer of mesh. Buy the sheets that have criss-cross hind-leg straps, as a rolling horse can easily dislodge the sheet if it's not held in place both in front and in back.

• You can poison the little wretches with pans of fly bait, set out of reach of animals and children.
• You can remove manure from the barn area, composting it to cook out the bugs, or spreading it to dry them out.
• You can purchase tiny "fly predator wasps" that hunt down fly larvae and kill them (very satisfying, morally).
• You can mist or fog the barn, by hand or automatically.
• You can paint your barn with insecticidal paint, either purchased as such (this type lasts longer) or as regular paint with an insecticidal additive. The idea is that the flies soak up the poison through their feet, and drop dead.