I'm switching from a 1999 Rock Hopper mountain bike to a new Jamis Aurora road bike. I want to move my cheapy security skewers over to the new bike, but they look a bit different from the skewers the new bike came with. Are all skewers compatible with all bikes, or are there different types?
Generally speaking, the answer is no. Not all skewers are compatible with all quick release wheels. There are different diameters and widths of skewers. Notably, many downhill bikes have beefier skewers that are built with a much larger diameter to be more durable. Bikes with wider and narrower axles will have less standard skewers too.
In your case, it is likely that the skewers will be compatible. Even if the skewer isn't quite long enough to have threads protruding from the nut, it will still be okay if the difference is less than 2mm.
See this forum post for more info:
True, the standard nowadays is 100mm up front and 130mm in the rear, BUT
When you start talking about different types of bikes, you get into different width hubs.
Tandems have a standard rear spacing of 140 or 145mm, some downhill/freeride bikes have a whopping 150mm rear spacing and 110mm front hub spacing and monstrous 20mm through bolt skewers, older bikes with French or Italian standards can have wacky sizes from 91mm 96mm, the list goes on.
But you are correct in saying the "standard" size for skewers is 100mm up front and 130mm in the rear.
They should be of a compatible width but its unlikely that they'll be the same length though. Most road hubs have different widths to MTB's. Fortunately for you, most road hubs are narrower and as long as there's enough thread on your skewer you'll probably be fine and should be able to just cut a bit off the end.