MySQL indexes creation strategy and inner logic - mysql

Question

This question expects a generic answer to the wide problematic of indexes creation on MySQL database.
Let's take this table example :
CREATE TABLE IF NOT EXISTS `article` (
`id` int(11) unsigned NOT NULL AUTO_INCREMENT,
`published` tinyint(1) NOT NULL DEFAULT '0',
`author_id` int(11) unsigned NOT NULL,
`modificator_id` int(11) unsigned DEFAULT NULL,
`category_id` int(11) unsigned DEFAULT NULL,
`title` varchar(200) COLLATE utf8_unicode_ci NOT NULL,
`headline` text COLLATE utf8_unicode_ci NOT NULL,
`content` text COLLATE utf8_unicode_ci NOT NULL,
`url_alias` varchar(50) COLLATE utf8_unicode_ci NOT NULL,
`priority` mediumint(11) unsigned NOT NULL DEFAULT '50',
`publication_date` datetime NOT NULL,
`creation_date` datetime NOT NULL,
`modification_date` datetime NOT NULL,
PRIMARY KEY (`id`)
);
Over such a sample there is a wide range of queries that could be performed on different criterions :
category_id
published
publication_date
e.g.:
SELECT id FROM article WHERE NOT published AND category_id = '2' ORDER BY publication_date;
On many tables you can see a wide range of state fields (like published here), date fields or reference fields (like author_id or category_id). What strategy should be picked to make indexes ?
Which can be developed under the following points:
Make an index on every fields that can be used in query (either as where argument or order by) even if this can lead to have a lot of indexes per table ?
Also make an index on fields that have only a small set of values like boolean or enum, this just does reduce the scope size of the scan by a n factor (assuming n being the number of inputs and every value homogeneously used) ?
I've read that MySQL prior to 5.0 used only one index per request how do the system picks it ? (by choosing the more restrictive one ?)
How does a OR statement is processed ?
How much does this is going to slow insert ?
Does InnoDB/MyISAM change anything to this problem ?
I know the EXPLAIN statement could be used to know whether a request is optimized or not, but a bit of concrete theoretical stuff would really be more constructive than a purely empirical approach !