
Grick |

In that situation, would a prone character have any penalties/bonuses on his ranged touch attack spell roll?
Prone: "The character is lying on the ground. A prone attacker has a –4 penalty on melee attack rolls and cannot use a ranged weapon (except for a crossbow). A prone defender gains a +4 bonus to Armor Class against ranged attacks, but takes a –4 penalty to AC against melee attacks."
If your DM allows firing a ray while prone, there is no penalty or bonus.
If your DM rules that a ray is a ranged weapon (perhaps due to this FAQ) then you can't do it at all.
-edit-
Using a non-Ray ranged touch attack is fine, as it's not a weapon. No bonus or penalty.

Grick |

I believe the spell was an Enervation spell.
Enervation is a ray.
If rays are ranged weapons, then you can't shoot it while prone.
If, when the FAQ says "rays are treated as weapons" it means only for the purposes of spells and abilities, then you can shoot it while prone with no bonuses or penalties.
Personally, I would lean towards the latter. It makes sense that it's hard to use a longbow while prone, but not so much to shoot a beam of magic out of your finger.