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At this point, we don't know any different. The change in mean Doppler shift of some stars with transiting planets as the planet covers pieces on different sides tells us that their orbits are more or less lined up with the star's equators (at least as opposed to being polar or retrograde). I've been told that the data exist to do slightly more in a statistical sense from the Doppler linewidths of stars with planets, but the analysis is tedious enough that the planet-hunting teams haven't been motivated to grind through it at this point (having plenty to do with new planets and all).
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Given the current theory on the Moon's origins, I would suspect its possible. However, the accretion disks remnant from the star's formation would almost have to have a prograde orbit. So if there are retrogrades, they're either captured orphans or suffered some kind of gonzo-level catastrophe that weirded their orbit out.
I'd be absolutely impressed to hear how a gas giant would manage to come off in a retrograde orbit. At that scale, it would want to play merry hell with the orbits of any other large planets in the system over the long term, robbing and transferring momentum, and whatnot, causing major chaos. A terrestrial or dwarf planet could be flung into a retrograde after a near capture by a migrating giant, but the big boys? I'll go ahead and throw money on the table that says if they're native to their home system, they're progrades.
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Lots of exosolar planets are in very elliptical orbits. This implies that they are also in highly inclined orbits due to the Kozai mechanism. So for these planets: no.
But I would guess that any system with planets in roughly circular orbits will likely orbit near the stellar rotational plane.
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