Cool idea - I plan on doing a Seattle to San Diego beer tour at some point.

I highly recommend the site BeerAdvocate.com for must-stops and non must-stops along the way. If you join, PM me here as I post there too.

I heartily second the recommendations of an earlier poster about Michigan and Wisconsin. Between Bell's, Founder's, The HopCat (beer-bar), and New Glarus, you've got the best beer in the Midwest.

Cheers and good luck,
Mike