Individual genome analysis tools
If you've received genotype data from us and are wondering what can be done with it, the 23andyou 3rd party tools page has ideas. If that selection is inadequate, you can use PLINK 1.9's --23file flag to convert your data to other formats.
Genome-wide association analysis
Our Statistical tests page has interactive browser binomial, Hardy-Weinberg equilibrium and Fisher 2x2/2x3 exact test p-value calculators, featuring a new algorithm capable of handling large input values at high speed without resorting to chi-square or other forms of approximation.
We have made minor contributions to the Reich Lab's EIGENSOFT package, and have posted prebuilt OS X and Windows binaries for version 5 at https://www.github.com/chrchang/eigensoft. (These platforms are not officially supported, but we'll respond to crash/bug reports as time allows.)