Like everything else, the "deposit" process is different at every dealer. My dealer will take a deposit at any time, so I put $1k down on one last March (yep, March '04). I have the receipt and the Salesman who I have purchased several vehicles from, and his manager both knew what it was for (since at that time, nobody knew if there would be a Cobra/Shelby/whatever). So, I am number 1 on their list, and last I heard they have about a dozen or so deposits already since the NY Show.
Incidently, they also put on the deposit receipt that I will pay "A-Plan price at time of delivery". So, no "Fair Market Adjustment" here.
Obviously, to each his own, but any dealer who decides to jack the prices out of the universe should be paid back by not selling any of them. I have to laugh at the dealers that had '03's on the lot for 18 months (and paid to have that inventory sit there) when dealer's like mine move the inventory, and folks like me don't even have to think about where to go for the new family car, truck, SUV, kids cars, etc. since we were taken care of the right way.
Just my .02 though, and YMMV.