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Perhaps the following can help your understanding.
Here's my super simplified breakdown.
The crontab is the default scheduler, if you want to say rotate your logs or run backups, at midnight. You would put that in your crontab.
A web server dishes out the web pages, and may get content from the app server.
In a typical three tier architecture it goes like this web server, app server, database server.
The app server has typically an application like webshere, weblogic etc etc. running on it and runs rules/business logic on what the user is doing.