Founding Fathers come in 5 flavors, with 5 matching flavors of points you can get. Whenever you explore the map, you gain exploration points, trading stuff gets you trading points, having cities and making liberty bells gets you political points, etc. Each founding father requires a certain amount of political points and whatever their native type is. (Peter Minuit is trading FF, so he also requires trade points.)
Whenever you collect enough points to get a founding father, he's offered to you. If you accept him, those points are deducted. If you decline, your points remain and you never can get him again. As you go up to higher numbers of points in each area, more FF are available.
The best FF far and away is Peter Minuit (Units cost 25% less to purchase in Europe). Obscenely, ridiculously so. Specialists are the key to the game's economy, and he gives them to you more quickly and cheaper. A core part of my opening is getting him. I trade to make sure I have enough points there and produce political points in my city(s) to get him ASAP, skipping all FFs before him, just to make sure I'm the one who gets him.
After him, the rest vary in quality from ok to useless, partly depending on your strategy. Vaco Nunez de Balboa (+25% defense per settlement) is decent, but the REF gets such large bonuses in city attack, its bad to defend in cities even with bonuses. You're better off fighting in the forests and mountains, both attack and defense, which makes Ethan Allen probably one of the most useful. Balboa's is really most useful in protecting you during the indian's sneak attacks.
Beyond that, its a matter of taste. Some are good for the LB spam period, particularly John Jay, Sam Adams, and Ben Franklin, and to an extent anyone who boosts LB production. Dom Pedro makes all your army like veteran soldiers, which is solid.
Thomas Paine helps with late military production, La Fayette and Madison help you pump out guns, Bermudez's faster ships are occasionally useful. Cabrel's shortened travel time to Europe is nice, but I always skip him since he's before Minuit.