depends on the beer. For five gallons of an American pale ale or saison, I have used the zest of 2-3 oranges with good results.
Yes, it depends on what flavors you would like in the beer you are making 
All snark aside, it really depends on what flavors you are going for in what type of beer. I have not used lime, though I've tasted beers made with a tincture of lime zest soaked in good tequila. Wasn't my thing. What I WOULD do with lime is make a Mexican lager (or cream ale) and use some of the zest at flameout.
You can add it at flameout, or make a tincture and add it after fermentation/at packaging. The advantage of the latter is you can do it to taste and scale it up (ie 0.5 tsp in 12 oz, would be 24 tsp in 48 12-oz bottles). On our next witbier, I want to experiment with adding zest and other aromatics during the whirlpool to steep in the hot wort.
no dumb questions here. I would continue to research on other forums, but good advice above on the nasty flavor of fermented orange juice. When the fructose ferments out, its basically all citric acid. If you wanted to make and bottle a shandy, I would advise chemically pasteurizing the beer prior to adding the oj/lemon juice (you can research that, but basically adding potassium sorbate and potassium metabisulfate...the problem becomes you can't carbonate in bottles, you would need kegging/force carbing equipment).
You've got awesome fruit, which many of us (especially those of us staring at snow) would love to have on hand. Out of the box thought, but have you ever researched making your own concentrate and freezing it in vacuum sealed bags?
