You can include page layouts for standard objects as part of your managed package, but they will not automatically take effect upon installation (i.e. the administrator must later go to the appropriate setup page and choose to use your layout). Organizations without the Record Types and Page Layouts feature (Team Edition and Professional Edition without this feature, the default) won't be able to see or choose your layout, and will need to manually recreate those layouts.
You may also include custom fields for standard objects, and they will behave normally. You should avoid using the External ID or Unique Index attribute, as those limits apply against the object across all namespaces and can cause installation failures. However, as above, these fields don't automatically appear on page layouts without some post-installation configuration. Some developers include a post-install configuration page that can make these changes automatically for orgs that have the appropriate API (Metadata API, specifically) to ease the post-installation process.