The rules you're looking for are in the weather section of DMG 3.5. On the page 95 the wind effects are described. The table 3-24 has a comprehensive list of wind effects for various wind speeds from light (0-10 mph) to tornado (175-300 mph) on creatures of each size. link
The effect can be one of the following:
Flying or airborne creatures are treated as one size category smaller than their actual size, so an airborne Gargantuan dragon is treated as Huge for purposes of wind effects.
Checked: Creatures are unable to move forward against the force of the wind. Flying creatures are blown back 1d6×5 feet.
Knocked Down: Creatures are knocked prone by the force of the wind. Flying creatures are instead blown back 1d6×10 feet.
Blown Away: Creatures on the ground are knocked prone and rolled 1d4×10 feet, taking 1d4 points of nonlethal damage per 10 feet. Flying creatures are blown back 2d6×10 feet and take 2d6 points of nonlethal damage due to battering and buffeting.
I don't know if there are rules for using wind to travel faster while flying, but you always can reverse the rules above or use rules for travelling downstream here.
If going downstream, add the speed of the current (typically 3 miles per hour) to the speed of the vehicle.