Does energy substitution cover force damage type?
I'd like to fire flaming missile to exploit monster weaknesses and searching for a way to add fire description to the spell or replace original with fire.
The Elven Spell Lore feat (from Player's Handbook 2) can change the damage type of one spell. In this case, Magic Missile. It requires either a high intelligence score or being an elf, and only works for prepared spellcasters with spellbooks.
For a more convoluted method, you can add fire damage to Magic Missile by using a combination of Snowcasting (from Frostburn. It adds the Cold descriptor to the spell) and Energy Substitution (which only requires the energy descriptor). This assumes that Energy Substitution changes the damage type of a spell to begin with - oddly enough, this is not stated.
No, Energy Substitution does not cover Force damage.
The feat states:
Emphasis mine. "An energy descriptor" is not a generally defined game term, as far as I am aware, so I'd say the only reasonable interpretation is the one that it is referring to the descriptors corresponding to the energy types specified in the previous sentence.
If you want a reliable, low-level spell that deals fire damage, I'd look at Lesser Orb of Fire, from Complete Arcane (reprinted in Spell Compendium).
Energy substitution only covers spells with "one type of energy (acid, cold, electricity, or fire)". Force (or sonic*) is not on the list.
As @Ernir found out, there are some metamagic feats that let you do what you wish (Snowcasting and Elven Spell Lore).
*while Sonic is a type of energy, the text can easily be read as "one of those types of energy (list)".