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Best index method ???

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Best index method ???
Ok, I am about to start a new web site project where I will be using Links SQL 2.2 in conjuction with a MySQL db. The version of MySQL that will be running on the server is 4.0.20.
My question is this...given the version I am using for both Links and MySQL, which would be the best indexing method to use given the fact that I plan on have a large amount of links (eventually).
I have read posts on this board on the subject but they all refer to older version of Links and MySQL.
Any input on this would be helpful.