A search engine operates, in the following order

1. Web crawling
2. Indexing
3. Searching

Web search engines work by storing information about many web pages, which they retrieve from the html itself. These pages are retrieved by a Web crawler (sometimes also known as a spider) — an automated Web browser which follows every link on the site. Exclusions can be made by the use of robots.txt. The contents of each page are then analyzed to determine how it should be indexed (for example, words are extracted from the titles, headings, or special fields called meta tags). Data about web pages are stored in an index database for use in later queries. A query can be a single word. The purpose of an index is to allow information to be found as quickly as possible. Some search engines, such as Google, store all or part of the source page (referred to as a cache) as well as information about the web pages, whereas others, such as AltaVista, store every word of every page they find. This cached page always holds the actual search text since it is the one that was actually indexed, so it can be very useful when the content of the current page has been updated and the search terms are no longer in it. This problem might be considered to be a mild form of linkrot, and Google's handling of it increases usability by satisfying user expectations that the search terms will be on the returned webpage. This satisfies the principle of least astonishment since the user normally expects the search terms to be on the returned pages. Increased search relevance makes these cached pages very useful, even beyond the fact that they may contain data that may no longer be available elsewhere.

When a user enters a query into a search engine (typically by using key words), the engine examines its index and provides a listing of best-matching web pages according to its criteria, usually with a short summary containing the document's title and sometimes parts of the text. The index is built from the information stored with the data and the method by which the information is indexed. Unfortunately, there is not one search engine that allows to search documents by date. Most search engines support the use of the boolean operators AND, OR and NOT to further specify the search query. Boolean operators are for literal searches that allow the user to refine and extend the terms of the search. The engine looks for the words or phrases exactly as entered. Some search engines provide an advanced feature called proximity search which allows users to define the distance between keywords. There is also concept-based searching where the research involves using statistical analysis on pages containing the words or phrases you search for. As well, natural language queries allow the user to type a question in the same form one would ask it to a human. A site like this would be ask.com.

The usefulness of a search engine depends on the relevance of the result set it gives back. While there may be millions of web pages that include a particular word or phrase, some pages may be more relevant, popular, or authoritative than others. Most search engines employ methods to rank the results to provide the "best" results first. How a search engine decides which pages are the best matches, and what order the results should be shown in, varies widely from one engine to another. The methods also change over time as Internet usage changes and new techniques evolve. There are two main types of search engine that have evolved: one is a system of predefined and hierarchically ordered keywords that humans have programmed extensively. The other is a system that generates an "inverted index" by analyzing texts it locates. This second form relies much more heavily on the computer itself to do the bulk of the work.

Most Web search engines are commercial ventures supported by advertising revenue and, as a result, some employ the practice of allowing advertisers to pay money to have their listings ranked higher in search results. Those search engines which do not accept money for their search engine results make money by running search related ads alongside the regular search engine results. The search engines make money every time someone clicks on one of these ads.

The opposites of overlinking are null linking and underlinking, which are phenomena in which hyperlinks are reduced to such a degree as to remove all pointers to a likely-needed context of an unusual term, in the text-area where the term occurs.[3] Underlinking results whenever a reader encounters an odd term in an article (perhaps not even for the first time), and wants to briefly browse more deeply at that point, but he or she cannot without an extensive search of the article for a (possibly non-existent) instance of the linked term.

The extreme case of underlinking is a dead-end page, a page with no links at all. Usability experts discourage making dead-end pages.[4]

Underlinking also occurs when web pages use the rel=nofollow attribute to prevent search engines from considering these links when performing link analysis, weighting or ranking.[5] Wikipedia is a well known example of this kind of underlinking.[6]

Search engines often use the number of backlinks that a website has as one of the most important factors for determining that website's search engine ranking. Google's description of their PageRank system, for instance, notes that Google interprets a link from page A to page B as a vote, by page A, for page B.[1] Knowledge of this form of search engine rankings has fueled a portion of the SEO industry commonly termed linkspam, where a company attempts to place as many inbound links as possible to their site regardless of the context of the originating site.

Websites often employ various techniques (called search engine optimization, usually shortened to SEO) to increase the number of backlinks pointing to their website. Some methods are free for use by everyone whereas some methods like linkbaiting requires quite a bit of planning and marketing to work. Some websites stumble upon "linkbaiting" naturally; the sites that are the first with a tidbit of 'breaking news' about a celebrity are good examples of that. When "linkbait" happens, many websites will link to the 'baiting' website because there is information there that is of extreme interest to a large number of people.

There are several factors that determine the value of a backlink. Backlinks from authoritative sites on a given topic are highly valuable. If both sites have content geared toward the keyword topic, the backlink is considered relevant and believed to have strong influence on the search engine rankings of the webpage granted the backlink. A backlink represents a favorable 'editorial vote' for the receiving webpage from another granting webpage. Another important factor is the anchor text of the backlink. Anchor text is the descriptive labeling of the hyperlink as it appears on a webpage. Search engine bots (i.e., spiders, crawlers, etc.) examine the anchor text to evaluate how relevant it is to the content on a webpage. Anchor text and webpage content congruency are highly weighted in search engine results page (SERP) rankings of your webpage with respect to any given keyword query by a search engine user.

Increasingly, inbound links are being weighed against link popularity and originating context. This transition is reducing the notion of one link, one vote in SEO, a trend proponents[who?] hope will help curb linkspam as a whole.

Leaving a comment on a blog can result in a relevant do follow link to the individual's website. Most of the time however leaving a comment on a blog turns into a no follow link, which is almost useless in the eyes of search engines such as Google and Yahoo. On the other hand, most blog comments get clicked on by the readers of the blog if the comment is well thought out and pertains to the discussion of the other commenters and the post on the blog.

Some links are created to intentionally hide the ultimate destination of a link until the user has clicked on it. It's accomplished via redirection (possibly a URL shortening service) or client-side JavaScript. Blind links are usually used for deceptive or advertising reasons, and are most associated with TGPs and Rickrolling.