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usually I recommend ht://dig. Yes, it takes time for indexing, but it got so many features (local characters, winword, pdf, fuzzy, synonyms, stemming, ...) and it's free.
If you don't want to go that way maybe the Altavista searchengine is ok. It sure is capable of index large sites, it supports a lot of file formats and it has a well known interface. (Although + and - are now common to all search services, incl. ht://dig).
Hope it helps.
I signed up for the 1000-page commercial version yesterday. ($300/yr). Works great, fast returns, good spider control, several easy-to-modify SERP templates. It took about 2 hours to have it going, including digging up the first 200 urls to be spidered. This will serve very well until I can get around to setting up a mysql index/search.
It has a fair site search term report, too.
>it's a lot easier to get rankings when you control the algo
Yeah, nothing like being the top 40 out of 40.