A human being should be able to change a diaper, plan an invasion, butcher a hog, conn a ship, design a building, write a sonnet, balance accounts, build a wall, set a bone, comfort the dying, take orders, give orders, cooperate, act alone, solve equations, analyze a new problem, pitch manure, program a computer, cook a tasty meal, fight efficiently, die gallantly. Specialization is for insects. - Robert A. Heinlein, Time Enough for Love... I suppose that does make it rather clear where I fall on this.
This post sort of follows some thoughts I've had a result of conversation with Somok over on his blog regarding the correct deployment of irritating monsters like golems.
This is a tricky subject. It is a problem with systems, a problem with players, and a problem with DMs.
The argument goes that golems are an unfair and unfun monster because the casters can't damage them directly, and because they negate the rogue's sneak attack. There is some basis to these complaints; I recall my first encounter with a flesh golem. I promptly hit it with a lightning bolt, which is precisely the wrong thing to do. We made it through but it wasn't pretty (and then there was a bodak in the next room! We all made all of our saves and had no idea the sort of peril we'd been in until later). So yes, for the unprepared caster, golems are a bad time.
The only excuse for a mid-level 3.x arcanist to be unprepared for such an eventuality, however, is ignorance. Even a specialist wizard still has access to most of the schools, and there are plenty of spells available from a variety of schools that work in a fight with a golem - displacement, haste, fly, sleet storm, and summon monster spring to mind immediately, just from the 3rd level list (and this is saying nothing of direct-damage SR-ignorers like acid arrow or the elemental orbs). Even if you don't want to learn and prepare spells for such an infrequent occurrence, scrolls are inexpensive and a good way to prepare for odd contingencies like golems. Nobody was tracking encumbrance anyway...
(Likewise, the rogue who takes some ranks in Use Magic Device can employ cheap, quarter-charged wands of low-level spells like Grease and Web to good effect. Lets you quit begging invisibility off of the wizard, too. This is one of the rogue's coolest abilities, but I don't think I've seen anyone use it in years)
So... why the frustration with golems, again?
Because players like to overspecialize. They (we) like to formulate their (our) tactics during character creation and pick abilities that support those tactics, often at the expense of any versatility and with full disregard for the maxim that "No plan survives contact with the enemy." When thrust into a situation where those tactics do not work, one of two things tends to happen: they either attempt to keep using them, to little effect, or sit on their hands and hope the situation changes. Either outcome is liable to lead to frustration.
This is the player part of the problem.
One of the system parts of the problem is that 3.x's buildiness encourages this. One of my favorite examples is the fighter and his feat chains. When was the last time you saw a 3.x fighter without Weapon Focus and Weapon Specialization? Spec is (considered) so good that it behooves you to specialize. If you've ever wondered why random treasure tables died out, Weapon Specialization certainly contributed. The two-weapon fighter has to sink a ton of feats into TWF, as well as picking ability scores to support those. There is a widespread belief that if you haven't taken Precise Shot, you shouldn't bother carrying a ranged weapon. That one particularly grinds my gears. My family has two sayings; from my mother, "No task is beneath you," and from my father, "Do what you have to do before what you want to do." Do you have proficiency with a ranged weapon? (Yes. Even monks get javelins, and druids get slings and Produce Flame.) It doesn't matter how bad your Dex or how low your BaB, sometimes there is a flying monster that needs shot down and today might just be your lucky day. This is a thing that you can do that improves the party's odds of winning - you should not hesitate to do it! It's alright to specialize, to be a master of one weapon, but it shouldn't stop you from using another when circumstances require it. Use what is useful, do what you can, rule out no avenue to victory.
All in all, though, the Player's Handbook material isn't that bad. Arcanist specialization is pretty lax, because specialist wizards don't lose all that much and Spell Focus' bonus isn't that big. Clerics come pre-specialized, which is unfortunate but at least you know what you're getting into and it's hard to restrict yourself much further. Overspecialization is mostly a fighter problem in Core/PHB, although the depth of the feat trees also bleeds into other mundane combatant classes.
Prestige classes are where it gets really bad, and possibly (I think) where the Overspecialist Syndrome began (my case of it at least; I claim no immunity. I also quite expect some AD&D grog to show up and comment about the Player's Option supplements and the kung-fu subsystem from Oriental Adventures). The whole notion of the prestige class, that you can sacrifice general capability in exchange for super-focused abilities, plays right to the overspecialist, and they're available for every class, in great heaping piles of splatbooks! The prestige class contributed, I think, to the commonly-held sentiment that every character should be a beautiful, mechanically-unique snowflake. With so many classes to choose from, there's no reason to ever play the same thing twice, or anything anyone else in your group has ever played before!
(Pathfinder, incidentally, has taken this past art and science to the realm of the mechanical process. When you start multiplying backgrounds/traits and all the wizard and sorcerer bloodlines and barbarian rage abilities and the new base classes they're pumping out, you don't even need prestige classes to be playing a unique, super-specialized character every campaign. Truly, they know their market.)
Of course, when we/I came down off the supplement high, this sentiment did not die despite the immediate dearth of prestige classes (God is dead but his shadows linger). So we brought it back to Tim's Trailblazer game, and there was discontent, because try as we might the Core rules didn't let us specialize as effectively as we were used to! It went pretty well for all that, and part of the reason for this, I think, was that Tim just wasn't pushing us that hard most of the time; it was OK to not be hyper-optimized, except inasmuch as you were competing with the rest of the party. There were certainly some nasty fights, but he did a good job of providing plenty of easier ones too, and wasn't out for blood (things I have been guilty of...). (Aside: Trailblazer almost got Weapon Specialization right by changing Focus, Spec, and ImpCrit to apply to a damage category (ie, Weapon Focus(Melee Piercing)), but then they went and screwed it all up with the fighter's Expert Weapon Proficiencies)
Prestige classes may have created the overspecialist, but it is the DM who keeps it alive. The DM part of the problem is observing the overspecialist's discontent and reformulating fights to avoid it rather than addressing it via communication. An entire campaign where most fights go according to the plan the PCs came up with three months ago is fundamentally boring as hell. Talk to the players, tell them that golems and flying monsters and paralyzers and charm/dominators and blinders and ambushers and really-high DR critters and incorporeals and fast monsters and lots of little monsters and really big monsters and enemy spellcasters are all on the table (and, hypothetically, maybe that save-or-die or gear destroyers like rust monsters aren't). Get them on board with it; discuss their motivations for overspecialization if you have to. "What're you really trying to achieve by playing a half-naga with four prestige classes who can only cast divination spells? If it's just an experiment, does that mean we can expect you to want to change characters when you get bored with it? If not, can we address your motivation in a way which is more useful to the party?" Make it an explicit social contract that if they build a character who can do exactly one thing, or play a character in a way that dramatically and unnecessarily limits their options, loss of fun is not a great and terrible injustice and is, in fact, sort of a personal problem, much like losing a chess match because you decided to only use knights. If part of the DM's job is to make sure everyone is having fun, then establishing realistic expectations regarding character usefulness necessarily follows.
Mechanically, let them prepare for a broad variety of threats. Don't restrict the availability of magical consumables for purchase. Let them shuffle their feats around. Whatever. Then just play the game and use enemies that make sense. If they're raiding the dwarven burial ground, any dwarf can tell them about the guardian golems and the dorfghouls. If they're travelling overland, any caravaneer can tell them about the manticores. Players in the generalist state of mind will usually find a way to deal with reasonably level-appropriateish things, especially if they're forewarned that these threats exist. The trick is showing them that playing without overspecializing can actually be fun, and that hyperspecialized character optimization is not typically necessary to fun or survival (or even conducive to either, in diverse environments).
(There's also, on further reflection, a group structure component to the problem - playing with large groups enables and encourages overspecialists, playing with small groups encourages generalists)