Tips
Some ideas about possible optimisations:
[edit] Optimising big deletes
If you want to do a big delete, say one which removes more than 50% of the rows in a table, you'll probably find that the table doesn't shrink (much) when you do it. Moreover, it might take quite a long time, especially if your table has many indexes.
A possible alternative would be to create a new table with the same schema, and transfer only the rows to KEEP in. Then rename the table with ALTER TABLE or RENAME TABLE.
This kind of thing can also be done with OPTIMIZE TABLE, but that could also be very slow.
[edit] ANALYZE vs ALTER TABLE
It appears that "ALTER TABLE Engine=MyISAM" does as much analysis as ANALYZE table, but unlike ANALYZE table, it doesn't block reads on the table while it's doing it. This may be helpful, especially if you need to do other alterations at the same time.