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SharePoint search features are managed at 3 levels

1. Farm level (configure the search service, configure crawler timeout settings etc…)
2. SSP (Shared Services Provider) level
3. Site collection level

The SSP functions are accessed via the Shared Services Administration.

SSP search functions:

• add sources to the crawl
• block URLs and URL patterns from the crawl
• define crawl schedules
• inspect crawl logs and troubleshoot crawls
• emergency removal of items
• install IFilters to support non-default file types
• add/remove file types from the crawl
• specify authoritative pages
• create scopes for all site collections (you can also create at a site collection level)

And in theory specify noise words and create a custom thesaurus.  See Inside the Index and Search Engines
chapter 5 for more.

You can by default index these types of content source:

• SharePoint sites
• Non-SharePoint websites
• Windows file shares
• Microsoft Exchange Server public folders (you can index exchange mailboxes with a 3rd party add-on)

Crawl management:

• Full crawl: indexes all content
• Incremental crawl: only accesses content that has been updated since last crawl. Faster, but slow if  accessing an external website
• Crawl schedules can be specified for each content source
• Crawls should be scheduled for low usage times

Crawl rules

• content can be excluded by defining a rule
• rules are applied in the specified order so you usually need to move exclude rules in front of include rules.
• a URL can be excluded by adding it as an exclude rule
• URL patterns can also be excluded and help keep the management of rules neat e.g. http://www.bbc.co.uk/* or http://www.amazon.co.uk/*/dp/*
• Exclude rules will remove any matched URLs during the next crawl
• If you need to remove a URL in an emergency you do this via “Search Result Removal” instead

Resources elsewhere:
Introduction to SharePoint Search Indexes for DPM Administrators
Enterprise Search administration