My favorite Flan always has that nice light brown sauce underneath, is there a way to prepare that from scratch?
That is simply caramelized sugar that coats the dish before the custard is poured in for baking. As the flan is chilled, the moisture from the custard liquefies the caramelized sugar and results in the sauce.
If you're wanting to make it for other desserts and aren't making flan, then simply caramelize sugar and then add water to it. Be careful as the steam can easily burn you if you're standing over it. The sugar will seize up and then as it continues to cook the crytallized caramelized sugar will liquefy. You will then have caramelized sugar syrup.
I've got a full recipe for flan here: http://www.herbivoracious.com/2009/09/burnt-sugar-flan-recipe.html . You can see from the picture there is plenty of sauce. Adjust the darkness by cooking it longer or shorter; I prefer it just short of burned.