Way back when I was running my own publicly accessible server, I changed the string to anonymous/service, so I only ended up as a "other" Netcraft statistic. You can change it in one of the include files (nsd.h, I think) then compile normally.
I'm not too sure about Netcraft's methodology and wouldn't really look at their statistics without a very large grain of salt. They admit to being thrown off by load balancers, etc. (try www.geocities.com). If sites like Geocities and Yahoo are running on a bunch of different OS + server software combinations behind load balancers, then they are not being properly represented in the Netcraft surveys (and I bet both sites have more than one machine apiece).
Nonetheless, Netcraft is a clever tool that occasionally comes in handy.