Let me chime in a with few thoughts, for whatever they're worth.
First of all, just so that everyone's on the same page: it is important to remember that the fermion masses, unlike the Higgs mass, are "technically natural" - that means that when their value is set by whatever mechanism sets them, they will not get pushed around much by the quantum corrections. This means that there is no "hierarchy problem" in the Yukawa sector - whatever the Yukawa couplings are, that's just what they are. You don't have to "fine-tune" anything.
Many of my colleagues have denied that the "flavor puzzle" is a real puzzle for this reason! I personally think that the flavor hierarchy is more interesting than that, but I feel that someone should mention that there are lots of very smart people who do not consider the large top quark a problem at all. After all: the Yukawa couplings EXPLICITLY break the flavor symmetry of the standard model. With this symmetry gone, what right do we have to expect there to be any pattern among the masses? That plus the fact that the disparate masses are stable to radiative corrections takes the wind out of the problem in many people's minds.
This game of playing with parameters can take us to many strange places. For example, if you are worried about the top Yukawa, why aren't you also worried about QCD? Why is the strong coupling so much less than electromagnetism? After all, why couldn't \Lambda_{\rm QCD} be only a tiny fraction of an eV? In such a case, you would still have asymptotic freedom, but the coupling would be MUCH less at room temperature - you would have free quarks, pions would be more analogous to hydrogen, etc. The fact that this is not the way nature works, and that \Lambda_{\rm QCD} is more like 200 MeV so that the QCD coupling is large, is not considered a "problem" among particle physicists. It's just the way nature decided to be.
There are some people who play the game of trying to get the SM parameters to work out. For example, you might have a brane world where there are a bunch of branes that intersect at just the right angles to give the strings just the right tensions to reproduce the masses of the fermions, etc. Maybe there is a "landscape" of possible worlds... Personally, I don't put much stake in this approach, but that's just me.
Furthermore, if you feel that there is something to the flavor puzzle, may I suggest that you actually have it backwords: that is, the top quark is the ONLY quark that has the EXPECTED Yukawa - all the other fermions are screwy! Why? Because the only scale in the problem is the Higgs vev, and therefore by dimensional analysis, we expect all the fermion masses should be that order. The fact that the electron is 10^6 times less than v suggests that there must be some new physics that introduces a bunch of small numbers that we don't know about. In fact, only the top quark has the "correct" mass.
Finally: a word of phenomenology. Everyone is in agreement that whether or not there is anything fundamentally special about the top quark, due to its large Yukawa coupling it will be the most sensitive probe of the physics of electroweak symmetry breaking. This is not (necessarely) because the top is special in the "eyes of God", but simply because the cross sections involving the top quark coupling to EWSB physics are larger than other probes. That is why, in my mind, people are so universally interested in the top.
Anyway, here are some of my thoughts on the flavor puzzle. I hope people find them enlightening.