Moth said:
I understand how it is possible to measure mass by deflection in a magnetic field or from resonances due to collisions. But estimating the mass of quarks by theory must be quite challenging. Also the Higgs boson, which not been seen, has been given an estimated mass of 120GeV, I assume is due to a theory.
The problem with the mass of the quarks (as has been alluded to but never explicitly stated) is that quarks are not "free particles" - they are always living in bound states. As you might know, the "mass" of a bound state particle is always lower than that of a free particle, since binding energy decreases it (the mass of positronium is LESS than 2m_e). Therefore, you can never isolate a quark to study its mass, since when we say that a quark decays, we really mean that the hadron the quark lives in decayed. The top quark is an exception to this because it decays before it has a chance to hadronize, and therefore there is a hope of doing a resonance analysis. The other "heavy quarks" (b,c) are heavy enough that you might hope to dis-entangle the QCD crap from the quark itself (remember, QCD is strong at low energies/masses); but this is a VERY dangerous game, wrought with theoretical difficulties ("renormalon ambiguities", for example). However, the "light quarks" (u,d,s) can never be separated from the QCD muck, and talking about their masses doesn't really make sense. For example: one book says m_u=3 GeV, another says m_u=300 GeV - since they're talking about different definitions of "quark mass"!
As to your other point about the Higgs: that comes from 2 places: (1) We haven't seen the Higgs boson yet, so it must be heavier than what we've been able to see (114 GeV), and precision electroweak measurements (higher order corrections in the perturbation theory) have been tested and suggest that the higgs cannot be much heavier than roughly 150 GeV. I should mention that BOTH of these constraints can be avoided, actually, and as I'm sure you know, the Higgs is still proving very elusive.
What kind of experiment would test a quark mass theory? For example I am currently using a program called calcHEP, which allows me to compute particle decay or collision properties. Do any of these experiments involve decays or collisions?
I think you misunderstood the phrase "quark mass theory". Like I said, you can NEVER truly measure the quark mass, except for the top quark.