With the tires being the same width and all else being equal, there is no perceptible difference.
However there are a few factors... based on information culled from forums etc.
1) Extremely slight preference to 26" for less wind resistance.
2) Extremely slight preference to 700c since it has to rotate slightly less, so less bearing resistance.
3) Extremely slight maneuverability improvement with 26" due to smaller diameter
4) Extremely slight better ability for 700c to deal with road imperfections due to larger diameter.
So... Basically, my understanding is that with everything being equal, you won't be able to tell a difference. However, bikes built for 26" and 700c are rarely identical.
You might make the best choice by exploring the other differences between the bikes you are considering and pretty much ignoring the wheel size.