It is not a good idea to use dedicated application pool for every web sites, Because every application pool consumes 8 MB of RAM. If you have 250 web sites, 250 x 8 MB = 2 GB of RAM is just required to manage your application pools.
You can split the application pools into a few part. Maybe,you can put the web site that requires much CPU or RAM recourse in a dedicated pool in order no to effect the others.
"scripts and executables" property allows the web sites to run cgi executables(.exe file).