From the SRD on critical hits -
Exception: Extra damage dice over and above a weapon’s normal damage is not multiplied when you score a critical hit.
From the Combat section of the 3.5e PHB -
Spells and Critical Hits:
A spell that requires an attack roll can score a critical hit. A spell attack that requires no attack roll cannot score a critical hit
From pg72 of Complete Arcane
Feats and Weaponlike Spells
Any spell that requires an attack roll and deals damage functions as a weapon in certain respects. As such, several feats that improve weapon performance can be used to enhance weaponlike spells.
The only thing critical hits do not multiply is bonus dice above and beyond the weapon's normal damage. The spell's base damage is the 'weapon' in this circumstance. Ergo, you would double the damage added from int, from Fiery Spell, from Weapon Specialization (Ranged Spells), etc, you're fine.
In Pathfinder, when you Empower a spell, you roll an additional half-sized die (like a d3, or a d2) for each empowered die. Those would probably be 'bonus dice', and therefore not be multiplied by a critical hit.
However, in 3.5, you just multiply the result of the spell's rolls by 1.5x, so it would stack with a critical hit.
Keep in mind how 3.5 handles multiplication, though - 1.5x + 2x = 2.5x, not 3.5x or the result of 1.5x + the result of 2x.
If you're using Sneak Attack to add +3d6 damage to a spell, that extra sneak attack damage would not be multiplied. Similarly extra dice from dragon fire inspiration or any other ability that adds 'bonus dice'.