Like they others have said, its case as well as socket location and cooler dependent.
I haven't looked at z97 boards but I assume that socket location and cooler choice shouldn't be as much of an issue as it use to be. Even in the z87 days the sockets were
moving up away from the PCIE slot. In the past some boards had the socket closer to the PCIE slot than the top edge and some larger air coolers would intrude into the PCIE space.
As for case issues make sure the case has space for 2 or more pcie brackets. Check the case for the location of fan mounts and/or vent holes. Remember the cards need air to stay cool.
Some cases may be better suited for blower style coolers(older reference style 290s) than open-air coolers(pretty much all currently sold 290s). Also determine the internal length
allowed for GPUs in the case and make sure the case is long enough for the card.
Remember: ITX requires more pre-purchase part planning since you have much less room to work with.