of course, use the language feature. Just create the other webshop as a 'new language'. Check this out, this is QC 3.1 free in action... this is hardware/software webshop: http://www.tigerware.sk/?sGoto=ag this is games webshop, in the same QC installation: http://www.tigerware.sk/?sGoto=ga
The obvious advantage is that orders come to the same administration, you don't have to visit different subdomains, etc. You can switch between the webshops via another QC advanced feature, the page redirection (please see the above examples on how it's done, look at the upper-most menu to see links on the AG and GA shops).