To answer the question rules-as-written:
Wherever the DM thinks appropriate. There appears to be no answer beyond that (especially nothing as specific as a table of default destinations) using official 3.5e materials - 3PP d20 material or earlier editions may be another matter.
For a more useful answer, we need to go beyond rules-as-written (which after all is the whole point of having a DM in the first place.) The best answer therefore depends on the style of game being played, of which there's infinite variation but here's a few ideas:
The narrative answer:
Wherever adds a good story twist, which probably means a populated area with NPCs to interact with. If it's the PCs first visit to that plane, a large city would probably be a good way to introduce them to the plane, as well as providing a useful home base. On the other hand, a small settlement would provide for more intimate interaction with local NPCs and lead to easier story hooks.
The conjectural cosmological physics answer:
The 3.5e Planar Handbook (p151) mentions planar breaches between planes, where the dividing line between two planes has worn thin. It follows that this would be a likely entry point to another plane, as the barrier between the two would provide the least resistance at these points. Planar material could be flowing in or out of this breach depending on the relative density of the planes concerned.
The Hollywood movie answer:
As mentioned in the opening question, there may well be a specific location on the destination plane that is related somehow to the point of origin of the travelers. Travelers from the plane of water may arrive in the middle of a lake or ocean, for example, while those coming from the plane of fire may arrive in a volcanic area.
To the best of my knowledge, there's no definitive list of these, and in many cases it's necessary to tweak the idea to something that would be appropriate on the destination plane - arrival from Mechanus may seem difficult to do if the destination doesn't have clockwork, but a ring of standing stones shaped like cogs feels like a good fit.
The random chance answer:
The DM grabs whatever maps or charts they have of the destination plane (sketching something out if necessary), makes up a grid reference scheme if needed, and rolls dice. Having a few easily adaptable generic maps at hand (with some locations that can easily be tailored to any plane) can be useful here. Tables would work equally well if preferred.
The murderhobo answer:
The PCs arrive at the entrance to the lair of planar monsters that need to be killed, because... they're not currently dead enough, and they have valuable stuff to take.
The "Teach them a lesson"/"My players are masochists" answer:
(Thanks to Zachiel for - unintentionally - reminding me to include this)
They arrive in the worst possible location. Covered in flames on the Plane of Fire, drowning on the Plane of Water, inside solid rock on the Plane of Earth, between two rotating cogs on Mechanus, five thousand feet above one of Arcadia's layers, etc. You'll probably never run into the problem of unspecified destinations ever again...
With a cursory search, I found a couple items. The reference I found indicated Heal Kits can come in +1 to +10, not just +2. I also found: Magic Item Compendium - Healing Belt – Gain a +2 competence to Heal Checks and has 3 healing charges. There are also Psionic Shards that can be up to +10 to a skill ability that can be applied to Heal.
I noted that these also have instructions on what it takes to craft the items. The belt for example requires Craft Wonderous Item, Cure Moderate Wounds, 500GP, 40XP and 1 day to craft. How much would the benefits and cost scale up if Cure Critical Wounds was used instead?
Using templates from existing items or the rules for crafting you could generate any number of items that can benefit your player character. You could also apply an item that grants a feat, or craft one and apply the feat Skill Master and specify Heal, this would provide a +10 to Heal Check.
Skill Mastery is also a feat the play could gain that grants a +10 to the skill. If you are writing the Prestige class you could incorporate Skill Mastery Heal as a special gained at a given level. You could possibly create an Improved Skill Mastery Heal that stacks for a second +10 if you want the PRC to have healing that powerful.
Hope you find this helpful.
Best Answer
There is something philosophical, no doubt, in the fact that this hinges on your definition of "reality."
There is no rule that limits this percentage to unity (100%), and all of the mathematical operations in which it is used work fine with percentages above it. So from that end, realer than real could be a thing.
The question, then, is whether "reality" is a game-term, defined exclusively by the rules of the (Shadow) spells, or not and defined as in real life. If the former, then realer-than-real spells are possible, and succeeding on a saving throw causes you to be more affected than failing. If the latter, it's a matter of what you think reality is; whether or not it has some essentially fake quality that something can be more real than it.
Strict RAW, it seems to be a game term, so your damaging spells deal more damage. Your non-damaging spells always work.
And it doesn't matter because every DM should ban reality-improving effects, particularly the shadowcraft mage, on sight. (Why? Because the spells are too versatile like that. It's basically spontaneously casting the entire Sor/Wiz list. Plus a shadowcraft mage can be optimized to cast any spell, from a cantrip (silent image used as shadow evocation for miracle).)