Very many thanks to all those who replied to my query about null alleles 
and population structure. I had around 50 answers, which is testament to 
the extent of the problem.

Shortly before my submission Chapuis & Estoup published a simulation of 
the effects of various ways of estimating the frequency of "the" null 
allele and adjusting Fst estimates. They have also developed software to 
do this, which will surely become an essential resource to many:

Chapuis & Estoup 2007. Microsatellite null alleles and estimation of 
population differentiation. Mol. Biol. Evol. 24: 621-631.

http://www.montpellier.inra.fr/URLB/

Cock van Oosterhout's MICROCHECKER (the current version is a major update 
from the last time I looked) applies one of these and is available here:

http://www.microchecker.hull.ac.uk/

van Oosterhout, C., D. Weetman, and W. F. Hutchinson. 2006. Estimation and 
adjustment of microsatellite null alleles in nonequilibrium populations. 
Mol Ecol Notes 6:255-256.

So, if you are prepared to live with the assumptions of these (the main 
ones being that your problem is due to a single null, and no Wahlund 
effects) there is great scope for Fst-style analyses.

A nice surprise to me is that an imminent release of STRUCTURE allows 
treating loci as dominant markers so allowing analyses of potential 
sub-structure despite nulls. This is not available yet, but is to be 
released soon on the STRUCTURE website and Daniel Falush and colleagues 
have a paper (again, just out) in MEN on this.

http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-8286.2007.01758.x

http://pritch.bsd.uchicago.edu/structure.html

It may be worth mentioning here that there are also methods for 
relatedness and parentage:

Wagner AP, Creel S, Kalinowski ST (2006) Estimating relatedness and 
relationships using microsatellite loci with null alleles. Heredity 
97:336-345.

I will not send all the responses I received out on EvolDir, as these are 
lengthy and the new developments bypass many of them, but I have compiled 
most of the answers here:

http://bio.st-and.ac.uk/supplemental/ritchie/NullResponses.html

I would like to finish with two nice quotes:

My instincts are to think a lot about the data, keep your eye on the 
biology and total evidence, and be prepared to argue your case with 
editors.  Sometimes they are unreasonable, but that can happen on any 
issue.
 	- Paul Sunnucks

If we combine our problems, maybe there is food for an article "S.O.S. - 
Save Our Samples: survival guide to get the best out of the worst". This 
might get a lot of citations.
 	- Dieter Anseeuw

Best wishes & thanks again,

 				Mike

Mike Ritchie                           Phone 0 (44 outside UK) 1334 463495
Environmental & Evolutionary Biology   Fax   0 (44 outside UK) 1334 463366
Dyers Brae House
University of St Andrews               E-mail mgr@st-andrews.ac.uk
St Andrews, Fife
Scotland KY16 9TH

Website:
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