There is not much comparison in handling and performance between the two. The Boxster justs feel better and more fun. If you need 4 seats(occasional back seat for 2 midgets) then the 996 is okay for that.
Not much difference in running costs between the two. Boxster slightly less but budget around $1500 to 2000 a year for expenses. If you are concerned about the ims then you will have to put out more to replace that.
I have tried to like the water cooled 911's but cannot sell my Box for something so GT like. Enjoy your search and try lots of cars. PPI is a must.
Cheers, G.