They tend to have PCIe form factors because it is a modern bus used in many high speed applications - I'm currently developing a PCIe Gen3x8 application around an Altera one.
But if you don't need the PCIe capability, it is possible to use these boards stand-alone. They tend to have external power supplies which can be used if not connected to a motherboard. You can also pretty easily remove the PCIe bracket from them and they can then be mounted horizontally on something.
If you do want PCIe, but only have a laptop, then this is possible too. You can get an Express Card to PCIe adapter (I've used the one from OneStopSystems). Be aware though, these are only single lane Gen1. In my current project, I've tried connecting my Gen3x8 design via one of these backplanes to a laptop and it correctly negotiates down to Gen1x1 and works perfectly (albeit considerably slower).
You can get development boards for USB 3.0 which are standalone - I think there is a cypress one for example. But USB, even 3.0, is generally much slower that the capabilities of the high end FPGAs - in fact many of the FPGAs can go faster than USB3 or PCIe3 can handle.
The other distinct advantage of PCIe over other buses, is most of the high end FPGAs already have CML transceivers built in to them, which means they can be interfaced directly to PCIe signals without the need for external ICs. Ethernet and USB on the other hand tend to require external PHY chips, so result in more complex (and expensive) designs.