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The stem that you decide on is generally a preference thing. Some riders are going to prefer a top load stem, while some riders are going to prefer a front load stem. As far as geometry, top load stems have rise. Most front load stems are virtually level.
What I mean by this, is that where your handlebars mount on the stem on a topload stem is higher than where they mount on a frontload stem. Now there are anomalies like the cinema projector stem and other stems with frontload construction but a slight degree of rise. But in general, your top load stem is going to put the bars taller up without actually having to buy taller bars.
Aside from that, topload stems have a whole different look. They look more slim and lanky, while the frontload stems looks square and bulky. You generally find a topload stem on a street rider's bike while the front load stem is found on a park rider's bike.
Sometimes companies hollow out frontload stems a lot more than topload stems in order to save weight. However, there is no clear conclusion on whether or not topload stems are lighter than frontload stems.
For me personally, I ride a topload stem. My handlebars are 8.9" tall so the rise from my topload stem makes them feel over 9 inches. And I didn't have to buy taller bars. I also think that the angle of the rise of the stem helps with barspins though this is not a proven fact.
If you want to learn everything that you can ever imagine about BMX pegs check out the Big Book of BMX Specs.