Use Custom Profiles Where Possible

Standard profiles are salesforce.com's intellectual property.  We will often make adjustments to these profiles permissions from release to release in order to introduce new functionality easily to our customers.  By cloning these profiles, you automatically inherit the new functionality and can always take it away later if you so choose. However, because standard profile permissions are unchangeable, active users assigned to these profiles will automatically inherit this functionality and you will not have the option to remove it unless you reassign those users.
Custom profiles do not typically change from release to release.  When you decide that the cloned Standard User profile should not have View Setup and Configuration, we will respect that change from release to release and leave that permission disabled.
Custom profiles are exactly that, custom.  Unlike standard profiles which do not allow you to adjust user or object permissions, you have full access to modify all permissions.
Standard profiles have their use, but you should limit that use to cloning if you have the ability to do so (Enterprise and Unlimited Editions). In Professional and Group Edition, you may only assign Standard Profiles and cannot customize them.  As a result, you cannot control your user's functional access beyond the assignment of a standard profile.

To clone a standard profile, go to Setup | Administrative Setup | Manage Users | Profiles and clone the next closest profile to what you need. If you are using Enhanced Profile List Views, you can create views into the user and object permissions in the profile to have a better sense of what the closest profile to your needs may be.

To assign a profile, go to a user's record and edit it to switch their profile. It is possible to automate this assignment across many users by using the Web Services API and a tool like the data loader; you will just need to know the profile id and the user id to assign the profile.