I need to host many (tens, hundreds) of small identical JAVA web applications that have different loads during one time.
For hundreds of webapps, you will very likely need more than one app server instance. But this sounds odd to be honest.
I want to use Glassfish V3. Do I need to use a load balancer and clusters or something else?
Right now, GlassFish v3 offers only basic clustering support using mod_jk (i.e. no load balancer plugin, no centralized admin, no high availibility). If you are interested, have a look at this note that describes the configuration steps of GFv3 and mod_jk.
For centralized admin and clustering, you'll have to wait for GlassFish 3.1 (see the GlassFish Roadmap Community Update slides).