Given your specific described scenario, I would most definitely take the comapny car, and what tips the scale for me is the uncertainty you have that he will be in the position for a period of time.
If you were very confident that he was going to be in this job for awhile, taking the $1000 and paying the car off in 3 years wouldn't be a bad deal at all, regardless of the mileage you will have. The car would still have a good amount of residual value left to trade in for another car, or you could keep it to replace a second car, etc.
However, since you seem to think there is a chance he might not be in the position for a long period of time, take the company car! Last thing you want is a $32,000 car payment with high mileage and no money coming in for it a year into your loan.
Also, the $1000 allowance will be taxed at your marginal tax rate I believe. My wife's company is getting rid of their comapany cars (Ford Taurus') and will be going to car allowances. She gets two options. The first would be to participate in a Runzheimer program that gives a base amount of $300/month, plus money on each company mile driven. The other option would be to take a straight $800 allowance with no provisions for mileage. The Runzheimer program is good in that it is tax free that way it is setup and run. The $800 allowance however has to be taxed.
We are going to choose the $800 allowance over the Runzheimer program as a majority of my wife's mileage is actually driving 35 miles each way to and from work, and thus does not count as business mileage. We think the $800 allowance, though taxable, will still wind up being the better deal given her driving patterns.
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