Since the thread is named "case study", here's three of them:
Study #1. Ftr 1/Wiz 6/Spellsword 1/Eldritch Knight 8. 14 strength, belt of giant strength +4, +1 holy adamantine guisarme of wounding (greater magic weaponed to +4).
Example 1A. Cornugon (CR 16 if you're counting). Flies in from hiding and lands 15 feet away, hoping to dominate the battlefield and not realizing that the fighter/wizard is carrying a reach weapon (or that he's a fighter wizard). On the fighter/wizard's initiative:
Cast wraithstrike, arcane strike fires of purity, activates his contingent greater blink spell, clicks on boots of speed, power attacks for 10 and makes a full attack for 2d4+30+6d4+1 point of con. By the fourth attack, the Cornugon was dead. Now, the cornugon at that point had a normal AC in the high 30s, but, against a blinking opponent, his touch AC was 9. Result: Dead cornugon.
Example 2b: Angel of decay approaches the same fighter/wizard. Player recognizes the monster description as something from Libris Mortis--he's not sure what; he just remembered it was one of the things he read and thought "you know, I'd rather not fight against that." So, he does the same thing. On the third attack, the angel of decay is no more.
Example 2: Ftr 1/Wiz 6/Eldritch Knight 10 Str 14, +1 axiomatic light flail of spell storing greater magic weaponed up to +4.
Example 2A.
Round 1: he shows up, casts otto's irresistable dance, and touches the barbarian. (out of the fight). The fighter charges him and does a leap attack, setting off his blink contingency.
Round 2, 3: The eldritch knight casts wraithstrike, arcane strikes a mid-level spell and drops him from his full 150+ hit points to single digits. He misses once due to blink and that saves the fighter. Fighter sucks up two heal spells from friendly clerics.
Round 4: Eldritch knight crits once and drops the fighter to -25 hit points or so.
Example 2B:
Round 1: the dwarf fighter sees the spellcaster and charges into the fray. The eldritch knight casts wraithstrike, arcane strikes his greater arcane sight and makes a full attack. The dwarf is left at about 15 hit points because the eldritch knight rolls a 1 on one attack. The eldritch knight's friends finish off the dwarf.
What's the same in all of these examples? A well defended foe who should be a challenge is dropped in a single full attack by a fighter/mage using wraithstrike.
Now, before deciding that wraithstrike is broken, let's consider a few objections:
1. It's not just wraithstrike. In the examples, you're considering wraithstrike, greater magic weapon, Arcane Strike (and a high level spell), Power Attack, a contingency spell with blink or greater blink, a strength boost item (in the first example; Weapon Focus and Improved Crit in the second), boots of speed (in the first example), and a powerful weapon all working together in a single full round action. Of course it's going to be powerful. After all, if you work out a way to make Power Attack, Leap Attack, Imrpoved Crit, Shock Trooper, Combat Brute, Elusive Target, Improved Sunder, a belt of Giant Strength, a good magic falchion, and Cleave all work together in one charge attack, it will look pretty broken too.
Answer: A. The example is much easier to pull off than the Shock Trooper/Combat Brute/Elusive Target example. It is not only applicable against foes using weapons when you charge; it is applicable on any full attack action and is still pretty darn effective on a single attack (or whirling blade spell). The ease with which the combo can be pulled off makes it less of a corner case and more of a balance issue.
Answer B. The problem in the example can be identified as wraithstrike. A good weapon, and standard items and feats like Power Attack or a belt of Giant Strength are to be expected at high levels and, as Examples 1 and 2 demonstrate, can mostly be added or removed without ruining the combo. Wraithstrike is the key. Remove blink and example 2b still works. Remove the boots of speed and example 2A & B work. The only basic elements of the combo are wraithstrike, Power Attack, and Arcane Strike. Removing Arcane Strike would nor remove the combo either--only depower it a little. Removing wraithstrike eliminates the problem and allows the danger to scale. (Without wraithstrike, the combo will still punish low AC creatures like advanced winter wolves, but normal defenses will function against it--the fighter with a high AC in mithral fullplate and the Cornugon are likely to survive.)
2. The example is really only problematic for fighter/wizards. It's fine for everyone else.
Answer A: who else can use it? Holy word may only be broken for clerics who put a little effort into boosting their caster level and operate in an all-good party, but it still damages high level play. Blasphemy may be primarily broken for half-fiends with a low CR/HD ratio or +1 CR/4 HD advancement, but, in those situations, it ruins games. If it's only problematic for the people who actually use it, then a spell is problematic.
Answer B: As others have pointed out, it's also pretty hideous for dragons, enlightened fists, or pretty much anyone who fights in melee and, by hook or by crook (or by having a Races of Stone runecaster in the party) manages to get the ability to cast the spell. Put an extended wraithstrike in a ring of spell storing and fighters and clerics will get in on the action too.
3. Sure, it's hideous, but high level spells are hideous too.
Answer: A: That might be a good answer if wraithstrike were high level--but it's not. It's 2nd level. If it were a 4th level spell, it might stand a chance of being balanced. As a 6th or 7th level spell, it might be balanced. (Or not). As a 2nd level spell, it's not balanced.
Answer B: Even the hideous high level spells have defenses against them. Spell resistance. Fire resistance. Saving throws. Etc. The empowered and maximized scorching ray will do a lot of damage (93 points of damage if all three rays hit) and an empowered disintegrate will do a lot too (10.5 per caster level) but the first is thwarted by fire resistance--even resistance 10 will drop it to 63 points--and the second can be nearly negated with a fort save. Otto's irresistable dance is hideous, but mind blank stops it, greater dispel magic can get rid of it, and it only lasts a few rounds. Against wraithstike, there is no spell resistance and DR doesn't go very far. The only way to increase your AC against the trick is dex or deflection which, in nearly every case other than the monk, rogue, and the will'o'the wisp won't crack 20--even at 17th level.