They try to explain the various product lines on the Paizo Pathfinder family page here.
Pathfinder Chronicles is actually a deprecated name, it's now called Pathfinder Campaign Setting for clarity.
- Pathfinder - the core game products, mainbooks mostly
- Pathfinder Adventure Path - the big 6-part linked campaigns
- Pathfinder Modules - the smaller traditional adventure modules, more standalone, only sometimes loosely linked to others
- Pathfinder Campaign Setting - was: Pathfinder Chronicles, mostly GM-focused setting info. Worldbooks, citybooks, maps, NPCs. Often heavier on fluff than crunch.
- Pathfinder Player Companion - was: Pathfinder Companion, mostly player-focused guides with additional crunch and player-safe setting info for a given race or country.
- Also Tales (novels), Miniatures (minis), and Organized Play (adventure scenarios for tournament play).
A lot of this was somewhat confusing and has undergone a couple revs of rebranding, so when you see "Pathfinder Chronicles Mini" it probably is just a legacy term from before there was a "Pathfinder Minis" line and they were lumped into Chronicles.
Thug Rogue
A build I recommend a lot on this site is the Thug Rogue.
The Thug is an archetype for the Rogue in pathfinder. It allows you to stack the Shaken condition from Intimidate up to Frightened. If you score well enough on Intimidate to make it last for four rounds or longer. With the Enforcer feat, you can Intimidate for free any time you use non-lethal damage. With the Swashbuckler archetype (stacks with Thug), you can swift action demoralize a certain number of times per day.
How is this relevant to what you want to do? Enter Shatter Defenses. It requires Weapon Focus and Dazzling Display, but once you have it, if you attack a Shaken or Frightened person, they are Flat-Footed against you until your next turn. Wham, bam, thank you ma'am.
Produce Flame
Produce Flame is a great spell. Much-maligned, people often forget that it isn't just for hurling fire bolts at people - the flame held in your hand can be used for melee touch attacks at no cost to the duration. Note that unlike spells such as shocking grasp or inflict light wounds, the 'charge' is not used up if you strike someone with the touch attack - this means you can potentially full-attack people with your palm of flame (although you can't dual wield it - i'd recommend actually using a non-lethal weapon like a sap (or an Improved Unarmed Strike) in your off-hand to trigger Enforcer/Thug/Shatter Defenses, before you go in for the kill with your murderpalm).
A druid dip gives you access to this fantastic spell, in addition to other goodies (like an Animal Companion who can trigger Flanking).
Best Answer
Strictly speaking, yes, there is a difference, though some speculate that even the authors neglect it
So rays are a specific thing. All rays require ranged touch attacks, but not everything that requires a ranged touch attack involves a ray: ray-effects are a subset of ranged-touch-attack-effects.
Thus, if something applies some benefit or penalty to a ray, it applies to ray of exhaustion but not to mark of the reptile god or to spells improved by Reach Spell.
Without such a bonus or penalty, though, there is nothing inherently special about rays vs. other ranged touch attacks. The attack roll is made in exactly the same way and so on.
As for Weapon Focus, the feat allows a special exception to the general requirement that you pick a weapon for the feat, to allow you to pick rays. Only rays (and unarmed strikes and grapples) are mentioned as being allowed, not other sorts of non-weapon attacks, including non-ray ranged-touch-attack spells, or melee-touch-attack spells for that matter. Thus, strictly speaking, you could take Weapon Focus (rays) and get a +1 to the attack roll made when casting ray of exhaustion, but you would not get that benefit with mark of the reptile god, nor is there any option for Weapon Focus that does let you get that bonus.
However, many tables just treat all ranged-touch-attack-effects as ray-effects and that works fine, and might even be what the authors intended. There is circumstantial evidence that authors used the terms fairly interchangeably, and cases where something is never called a ray-effect, but seem like they’re supposed to be. This thread on Weapon Focus and ranged touch attacks confirms this confusion, and has many suggest that they treat the two as the same thing.
Note that in 3.5, Complete Arcane specified that all attack-roll using spells were considered “weapon-like spells” and “touch attack” and “ranged touch attack” were considered the two categories of such weapon-like spells for the purposes of Weapon Focus (presumably the spells that used regular, non-touch attacks like iron scarf were also included despite the name). While the same confusion about whether or not rays were synonymous with ranged-touch-attack existed in 3.5, the fact that 3.5 ran things this way without problems suggests that it is generally safe to do so.