Rays and ranged touch spells have three important differences.
There are three major differences between ranged touch spells and rays: Who you can target, what potential penalties there are, and what feats and abilities you can take to help.
Who you can target.
The rules on aiming a spell say:
Some spells have a target or targets. You cast these spells on creatures or objects, as defined by the spell itself. You must be able to see or touch the target, and you must specifically choose that target. You do not have to select your target until you finish casting the spell.
They then go on to say for rays:
You aim a ray as if using a ranged weapon, though typically you make a ranged touch attack rather than a normal ranged attack. As with a ranged weapon, you can fire into the dark or at an invisible creature and hope you hit something. You don't have to see the creature you're trying to hit, as you do with a targeted spell. Intervening creatures and obstacles, however, can block your line of sight or provide cover for the creature at which you're aiming.
In other words, if you can't see your target, whether due to fog, invisibility, or otherwise, you can't choose them as the target of a ranged attack. However, you can try to target them with a ray, the same as you can fire an arrow at where you think they are.
What potential penalties there are.
Going back to the ray description, you'll notice that rays are aimed "as if using a ranged weapon" and that creatures can block your sight or provide cover. In other words, if your allies are standing between you and your target, a ranged touch spell won't have a problem, but a ray will give the target +4 to their touch AC. Likewise, the concealment miss chance applies to rays if you can only partly see your target, but not ranged touch attacks.
What feats and abilities you can take to help.
As KRyan noted, you can take Weapon Focus to help with your ray attacks, but not your ranged touch attacks. According to the FAQ, you can also take Weapon Specialization and Improved Critical for rays. Presumably, other weapon-specific feats would also be applicable, although that's not explicitly called out anywhere.
Additionally, things that boost weapon damage like inspire courage will also boost HP damage from a ray but not a ranged touch. You can also sneak attack with a ray, but not a ranged touch, although when you do, you only add the damage to one ray.