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A search engine is either one of two things. It is a Robot, shown as letter "R" in Eureka!, or it is a directory, shown as a "D". A few search engines combine some features of both, but they are fundamentally one or the other.
You don't have to understand how or why they do these things. You only have to understand that they do them differently and produce different results. This means you have to use most of the major ones if you really want to find something.
Directory search engines don't look for anything on the internet to obtain the information they contain. They get the information from people who enter it into the search engines database. Some directories collect more or less types of information than other directories. Each directory has its own methods of categorizing the information. This is why there are so many directories. You may be maintaining your own directory in the form of a list of bookmarks or in a hotlist. If you aren't, you probably will.
You don't need to understand what these directories collect or how they organize it. You just need to know they will look at the website or internet resource and get different things and produce different results for the same thing when you use them in a search. Again, this means you have to use most of the major ones if you really want to find something.
There are relatively few guides on the internet because it takes a lot of time and energy to build and maintain them. The guides are like the general directories in that they contain relatively small amounts of internet information resources, but they are usually of relatively high quality. They are a guide to the top sites for you to visit.
A few newsgroups are moderated. This means their content is controlled by a moderator and they are very discriminating in what they allow to be posted in content and/or quality. They also eliminate duplicate postings. The newsgroups are like the robots in that they contain a large amount of information often with a lot of junk among the jewels.
Robots collect everything and anything, the junk as well as the jewels of internet information. The directories strive to collect mostly jewels, although some are more discriminating than others. In fact, you'll find some directories that are totally indiscriminate and evaluate a web site no more than a robot does. Some robots are more discriminating than other robots.
The thing you have to keep in mind when using these search tools is this. If you are looking for a subject that is of broad and general interest, like computer software, you should focus your search first on using directories. If you are looking for something that is rare or esoteric, like the postage stamps of New Zealand in the 1920's, you should start your search with the robots first. This is why Eureka! informs you if a search engine is a robot (R), directory (D), guide (G) or newsgroup (N).
These multisearch engines can be real time savers and very convenient, but don't forget that you are giving up all of the control on the search parameters to the multisearch engine which may compromise the quality of the results obtained. If you really must find out everything and/or a very specific thing on your search topic, you may be better off doing the individual searches yourself.
I do not want to suggest that you would be wasting your time by using these other search engines. On the contrary, these other search engines can be very useful. Most of them are very special purpose. For example they may contain only zip codes, or only telephone numbers, or only software products, or shopping malls, or local commercial sites, or restaurants, or hotels, or information about working with HTML. If the engine contains the information you need, that is the best place to look for it.
In fact, my own search engine, Silicon Valley Web Directory, is limited in scope to the greater San Francisco bay area and to the computer and semiconductor industry. This is absolutely the best resource for finding web resources about the Bay Area or Computer companies. I have just recently included it in Eureka!, but before that you could have easily found it using most of the search engines in Eureka!. There are many excellent search resources you won't find listed in Eureka!, but which you can find using Eureka! So don't worry about all those other search engines. You can get there from here.
Eureka! does not contain a long list of search engines because you can easily find them with Eureka! when you need them. You use this search engine to find those search engines and then you continue your more refined search using them.