Ahram Center, whose polls indicate that Moussa has a large lead, uses the best methodology as far as I can tell - given that they do face to face interviews whereas the others do telephone calls. The issue is that they do not provide details about the demographic breakdown of their sample size (particularly important is the economic breakdown).
However, the other two polls indicate that Shafiq will likely be the victor (or at least garner the most votes in first round). It is important to note though that these two polls also indicate that they derive much of their sample from the higher socio-economic portion of society - which is not directly indicative of Egypt as a whole. (Nevertheless, remember that it is voting people that count so if the voting population tends to be higher income, then these polls will be closer to reality).
One likely expanation for the large differences between Ahram and others is that, it seems, Ahram polls do not appear to give the option of undecided. They seemed to do that in some of the polls (4/27 and 5/11 polls) but even then the figure was around 11%-12%, far below the figures seen in the other polls. Again, poll results are largely dependent on the questions you ask and how you ask them - I would assume that is likely in play here.
For those who think polls in Egypt are useless, the below may help provide you with some backup for that.
For those who think the polls are useful, the data below may provide some useful insights.
(Click on images for larger versions...) To see preliminary results of Egyptian votes from abroad please click here