The Mayan long count is a cyclical system. We are presently in the 13th baktun of the current pictun (20 baktuns) which ends on the 21st of December 2012 of the Gregorian calendar, we then simply begin the 14th baktun.
There are NO Mayan prophecies related to the end of baktun 13, however they do mention that on the last day of baktun 14 a great celebration will be held to honour the workings of a great king.
By the time the Spanish arrived in South America no-one was using the long count system to mark time anymore anyway.
Now for the "other" threats.
Polar inversion, this happens quite frequently in geographic terms and hasn't once destroyed the world, moreover the magnetic poles are moving all the time anyway which is why the value for adjusting magnetic North to calculate grid North changes. Magnetic North pole is several miles away from where it was 100 years ago.
Planetary alignment, there are no planetary alignments that will coincide with 2012. Similarly there will be no alignment between the earth, the sun and the galactic core in 2012 anymore than there is every year as the earth orbits the sun.
Planetary collision, there are no planetary bodies on a collision course with us that would impact in 2012, although we are due to be whalloped pretty hard by a large asteroid sometime soon this could happen any day at any time and is no more likely in 2012 than it is today. You have a better chance of being killed by an asteroid impact than winning the UK national lottery even though no-one has ever been killed by an asteroid strike in all recorded history (however a dog was killed when a meteorite struck a building it was in), then again you are more likely to die going fishing, walking on stairs, driving a car or taking a bath.
While I admit, the idea of an extinct ancient civilization predicting the future by means of a lost knowledge is appealing somehow, the Mayans clearly did not predict the end of the world, they even managed to miss their own extinction at the hands of the Spanish so if they failed to predict the existence of humans other than themselves how could they possibly have foreseen the end of the world some 600 or so years after their own demise.