Very basically: low pins are good for rolly designs (oil balls), while huge pin-outs tend to have a more pronounced mass bias and therefore enhance flippy ball and drilling designs. But that's just a rough rule of thumb. Mostly, pin-ins have to be drilled for a rolly design (pin under fingers) to keep the ball legal, so it is wise to chose a ball base that fits the technical "framework" and matches lane conditions. Hope this helps as a first step.
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DizzyFugu --- Reporting from Germany
Team "X": http://homepage.mac.com/timlinked/
"All that we see or seem, is but a dream within a dream..." - Edgar Allen Poe

The answer to the question of what pin length depends on two things:

1) Does the ball have an asymmetric core?
2) How do you want to lay it out (i.e. where do you want the pin)?

If the ball is an asym, then the location of the cg relative to the pin matters less than with a symmetric core. With asyms, the mass bias associated with the second preferred spin axis is created mostly by the asymmetric core, not the cg/topweight. Therefore, with an asym, simply ask yourself where you want to place the pin and mass bias, then get a pin length/cg position that will allow you to place the cg close to the center of your grip.

If the ball has a symmetric core, then the mass that creates the second spin axis is the cg/topweight itself. (The second spin axis is 6.75" from the pin through the cg.) Therefore, the location of the cg relative to the pin is more important with a symmetric core. All else equal, a shorter pin length creates a smaller mass bias and creates less track flare. A longer pin length creates a greater mass bias and creates more track flare.

Think of the cg/topweight as putting leverage on the side of the core. At 90 degrees from the core axis (pin) is where the cg could place the most leverage. 90 degrees on a bowling ball is 6.75". A cg further away from the top of the core (pin) creates more leverage on the side of the core.

CK

One thing to consider is your ball track.  I track high so on symmetrical balls I keep the pin above the finger line.  On asymmetrical balls I can put the pin below the fingers because asymmetrical balls tend lower my ball track.

Another thing for me is smaller pins on asymmetrical balls tend to work better for me.  Tracks asymmetrical balls like the Animal worked really good for me with the pin below the finger line.  

If your going to choose a lyout with the pin above the fingers go with a longer pin out ball and if your going to put the pin below the finger line go with shorter pin out balls.

I hope this helps.