Spells are probably the trickiest facet of restoring some magic to the magic system. You can't very well keep the game mechanics of spells secret from players running magic-users and clerics. I think it's still possible at least to take the spotlight off of them, though, and re-center the focus on magic rather than numbers. Here are my thoughts on applying yesterday's points to spell casting for PCs and NPCs.
Scarcity: The most obvious first step is to make NPC spell casters, particularly high level ones, uncommon and difficult to access. Powerful spell casters have their own interests and agendas to attend to, and that shouldn't include being a spell vending machine to every peasant or wandering hooligan with coin to spend. Clerics may be subject to rigorous strictures regarding when and for whom they perform miracles, their magic reserved for uses that advance the goals of the faith. High level wizards go to great lengths to avoid distractions from their arcane research. In short, if the PCs aren't high enough level to cast a particular spell themselves, getting someone else to do it should require a lot of persuasion and a sizable favor, at minimum.
Another issue to address under the scarcity heading is player character access to spells. PC magic-users will probably find spell scrolls among the treasure hoards, and have opportunities to capture the spell books of defeated enemy mages. In the past I've simply allowed PCs to scribe spells found in books and scrolls into their own books, but this can quickly lead to every character knowing every spell, and whatever spells you give to magic-using opponents will wind up in the party's arsenal in short order. Sure, you can handcuff yourself by strictly limiting spell casting enemies, or come up with endless excuses as to why the defeated wizard's spell book can't be found or self-destructs and have your players feel cheated, but neither of those are much fun.
So, from now on, having a scroll or spell only assists a caster in researching the spell. Spells in a spell book are not a straightforward list of the words to be spoken in casting, but rather notes, scribbled equations, diagrams, bits of magical theory, mnemonic devices that help a particular wizard remember things, and so on. In order to scribe the spell into his own book, a PC spell caster must really understand the nuts and bolts of it and build his own version of it. A spell book containing the spell will count as the library requirement as explained in the Spell Research sections of the rules. The formula from the Rules Cyclopedia is: (Caster's level + casters Intelligence) x2 - spell level x3 = Percentage chance of success; cost 1,000 gp per spell level, requires one week plus one day per spell level.
Having a book with the actual spell, rather than just tomes of general magic theory, might grant a bonus, but the point is that the character will still have to spend the money, put in the time, and roll the dice to see if he succeeds in understanding the spell well enough to add it to his repertoire.
If a spell is a recipe, a spell scroll is a cake mix - one shot, ready to use. It doesn't in and of itself convey anything about the recipe. The caster must break it down and analyze it to learn that, which consumes the scroll in the process. I might allow a bonus to the chance to learn the spell from a scroll, since if it fails, the source material is gone and there's no second chance.
PCs in the same party may trade spells among themselves with the same nonchalance that players borrow books from each other. If you want to curtail that practice, apply the same rules, but add the teacher's level to the chance of success, and halve the money cost. You still have to pay for reagents, after all.
Description: Here's where magic can really come alive. Emphasize how the spell looks, sounds, feels (smells, tastes?) to the characters, rather than the mechanical effect it has on them. What does it feel like to be hit by a magic missile? Is it painful like being burned, shocked, stabbed, bludgeoned? Does it sting like a whip or cause a numbing sensation? Does it lacerate, bruise, or leave no marks at all?
"A tiny, twirling ring of gold sparks shoots from the wizard's fingertips, striking you with a sharp, stinging CRACK! You take five points of damage, as a momentary wave of nausea sweeps through you," is probably going to unnerve a player more than, "He casts a magic missile at you. Take five points of damage."
This could be especially fun with spells that have no obvious visual components. ESP might give the target (or the caster!) a brief headache. Dispel magic might sound like a bubble popping, Protection from Evil could give a little surge of euphoria. Skin prickling, chills, a flush of heat, the scent of ozone or of hot metal or fresh-cut grass, an itch, a flash of emotion, whatever seems to go with the spell in your mind. Secondary sensory effects don't have to be limited to caster and target. Those nearby when the spell is cast might feel something as well. (This might be a fun way to warn/scare the party when a particularly dreaded spell is being cast, and really make that next initiative roll important to them!)
Keep game mechanics away from players: Tell the players how the spells affecting them make them feel, and apply the mechanical effects behind the DM screen. You don't have to tell the player that the Blight spell gives him -1 to hit, just tell him that he feels unnerved or weakened or whatever and mentally subtract it from his rolls. It isn't possible with every spell, but a good many of them can be handled this way. I'm going to do this even when it's a spell cast by an ally, who knows the pluses and minuses of it, simply to shift the focus as much as possible.
Secret notes are a great way to keep knowledge from the rest of the table while sharing it with the player who needs to know. If the evil priest casts Hold Person on someone's character, slip her a note requesting a saving throw, and her compatriots won't know for sure why her fighter just toppled and lies motionless on the ground with a blank, frozen stare. Is she dead, unconscious, poisoned, paralyzed, or something else? Should they check on her now and try to help her, fight on and hope she recovers when the battle is over, or is she beyond help already? What should they prepare their defenses against to keep from sharing her fate in the next round? Keep as much of the unknown as you can, well...unknown. Almost needless to say, secret notes really lend themselves well to charm spells!
Variation: The obvious one here is to arm your NPCs with spells to which the player characters don't (yet) have access. Other editions of the game are fertile sources. The Dragonsfoot forums and the Ancient Vaults and Eldritch Secrets blog have lots of cool stuff too.
The less obvious (and potentially more fun!) way is to give NPCs custom re-fluffed variations of familiar spells. Brilliant blue or pink fireballs, magic missiles that look like spinning saw blades of white light or nearly invisible distortions in the air like a ripple of heat? Sure! Does that wizard's Web spell come out as a random mass of sticky strands, or like the orderly web of an orb spider? Does his Shield make an invisible barrier, or does it conjure a floating knight's shield that parries attacks? A cleric's Hold Person might have a visual component, perhaps a crackle of electricity that zaps the target like a taser, or a silvery ethereal rope that wraps it from head to toe. Remember how many different Water Breathing effects the Tri-Wizard Tournament contestants used in Harry Potter and the Goblet of Fire? When you don't call the spell by its rulebook name, "re-skinning" the same mechanical effect with a different description can make it seem completely unfamiliar and mysterious.
Conditions: Alright, this one is a bit tough to apply to spells, but it can be done occasionally. Magic zones in the dungeon or wilderness where spells don't function quite as they should are one possibility. Modifying spell descriptions to include conditions is another, though it requires some thought and work. Making spells have unusual effects under very specific conditions that the players might discover by accident or rumor are still another. Maybe rust monsters are vulnerable to Heat Metal, or large masses of metal within 50 feet will draw off a Lightning Bolt just like a lightning rod and zap anyone within 5 feet of it, rather than the intended targets. Perhaps there's a certain type of mold that causes magic missiles cast nearby to splinter into tiny missiles that do 1 point of damage each. There could be some magical ore that makes detection spells go haywire. What if you CAN charm an undead creature, but only when a full moon occurs on the anniversary of its death? Is there a danger of reflection when casting spells from air at a target under water or vice versa?
This is getting overly long, so I'll wrap it up here. Next up, Magical Magic III, Arms and Armor.