It doesn't really make any difference, as such.
If you want an omni directional pattern from your antenna, you'll almost certainly want to use vertical polarizationm, just because most "omni" antennas are only omni directional when they are vertical.
But all that actually matters is that the polarization of the receive antenna matches that of the received signal. And note that the polarization of the signal isn't necessarily exactly the same as the transmit antenna either! If the signal bounces off a few strange objects (aluminum foil backed insulation in walls is a very nice reflector, for example) there may be some changes, depending on the angle of the reflections.
There are a couple of practical ways you can use that information. One is that if you can use horizontal polarization (for example if you only have two units, and this would be very applicable if one is on a different floor than the other), it might provide you some isolation from other nearby wifi radios, almost all of which are going to be using vertical polarization. Typically there can be a 25 to 35 dB difference vertical and horizontal polarization, if there are no other factors.
Another practical thing to do is adjust the angle of one antenna while checking the signal strength. Just because the other antenna is vertical doesn't mean, for example, that a PCI card with a wifi antenna sticking out the back of a desktop machine is going to get the best signal with that antenna in a vertical position. Move it around and see where it does get the best signal.