The Mystic Theurge (MT) prestige class has been the subject of some second looks lately. On the Wizards of the Coast site, there has been a Design Diary and a Tips article on getting the best bang out of your MT buck. Naturally, I feel that I have something to say on the topic, so let me give you my two copper pieces (plus some links to other MT goodness online).
To start out with, here is the SRD Mystic Theurge. Wizards has an online version with all the original flavor text. As the closest thing 3E D&D has to the old first and second edition magic-user/cleric, how do you get the most out of your MT? Let's take the major options and tactics one by one.
Which Base Classes?
You need both arcane caster class levels and divine caster class levels to qualify for the MT PrC. But which classes should you pick? Consider that in any caster class, there is a mix of spell casting and everything else. If the "everything else" is meager (as for the Sorcerer), then the spell casting is potent. If the everything else is fantastic (as for the Bard), then the spell casting is weaker.
MT progression advances your spell casting and cuts out the "everything else." If you have a lot of "everything else," think twice before you take the MT.
That said, the Sorcerer is a good choice for base arcane because he loses nothing (except familiar advancement) by taking MT levels. The Wizard, on the other hand, gives up bonus feats otherwise gained every five levels. BUT -- to qualify for the PrC, you have to take four levels of Sorcerer, but only three of Wizard. Is jumping into the prestige class a level earlier worth casting fewer spells (you would get more spells to cast as a Sorcerer MT) or worth giving up the four bonus feats (you would have gained them at levels 5, 10, 15, and 20 as a pure Wizard)? Personally, I think it is a wash ... pick whichever appeals to you on a flavor and role-play basis.
But it is clear that if you strip a Bard of bardic music and lore advancement and thrust him into one half of an MT, you lose out power-wise versus either the Wizard or the Sorcerer, by quite a margin. So I don't understand this line in the Wizards of the Coast Tips article "bard/mystic theurges make great support characters fully able to use their bardic music and spells to boost their companions." Is the writer, Creighton Broadhurst, saying that MT levels stack with bard levels for advancing bardic music? I do not think that is true ... but I'll write to Wizards and we'll see what they say.
The case is clearer for divine casters. Paladin and Ranger casting is so minor that it is clearly not a good option for MT advancement. Druids get a lot more "everything else" than clerics (Wildshape, Animal Companion, etc), and it follows that Druid spellcasting is not as potent as Cleric casting. The Cleric MT is the better choice from a power-standpoint.
(Full disclosure: I must note that I play a liontaur Bard/Druid online! And soon he'll take up a homebrew Seer prestige class, which advances spell casting in both classes, like the MT. My Seer, though, stacks with Bard for lore and music and grants some nifty powers. On the other hand, it restricts the caster to ONLY enchantment and divination spells! Yes, Zeoll is still a little under-powered vs a Wizard/Cleric, but I made my choices for role play reasons, and I'm happy about him.)
Which Two Domains?
If your campaign requires you to select a god, then you obviously have limited choices, since you are restricted to those domain options allowed under the campaign gods. But your DM may allow you to pick a philosophy or other object of veneration (like Banjo the Clown, say), giving you the choice of any two domains.
As a Cleric, what should you pick for those two domains? There's no need to weigh very heavily the possible expanded range of spells that a domain adds to a Cleric's spell list, since as a Wizard or Sorcerer you have choices galore. So look at the granted power. There are two kinds of granted power: ones that improve with class level (Water domain's special turning, for example) and ones that grant a one-shot ability (Luck domain's reroll, say). Since your class level will go to three and stop, do not pick a domain that advances with class level! For example, you might be tempted by the Magic domain for the synergy with your Wizard levels, but all that three cleric levels give you is a +1 on arcane scroll casting. Not really very impressive.
Consider the domains that are not cleric-level dependent. War gives you two feats (a martial weapon and weapon focus), but the value of that varies with how much you expect to be rolling attack dice. Luck gives you that great reroll ... especially sweet if your DM lets you reroll hit dice. Healing gives an extra +1 on Cure spells and extra healing as domain spells, which is good if you plan to fill the traditional cleric role (especially if you are the party's only cleric). Knowledge boosts caster level by 1 on all divinations, an especially nice option if your Wizard is a Diviner. Good gives you an extra caster level (and thus an extra round of duration) when you summmon good creatures ... Good and Law (or Good and Chaos) give you an extra TWO rounds on LG (CG) creatures, so if you go the Summoner route, it's an option. Those extra two rounds of duration are swell at low level, but as you get more experienced (and as your summons have longer durations), that's less of a factor. YMMV.
What About Armor?
It is a real shame to waste your sweet clerical armor proficiencies just because of arcane spell failure. You might want to consider being an Arcane Tank. Armor yourself up real good and focus on verbal-only arcane spells (or on arcane spells that have a long duration, like Shrink Item, that you can cast before putting on armor. Take the Still Spell feat for one of your slots.
Even if you do not wear armor, consider buying a mithril buckler or a mithril small shield -- it has zero percent arcane spell failure!
Pick a Strategy. Pick Three!
Your strength as a MT is versatility. Don't get trapped into the mindset of being only a Healer or a Buffer or a Summoner or a Blaster. Instead, since you have so many spells to cast, have several strategies ready, depending on circumstance. If you are an Arcane Tank, at the start of encounters, be ready with Diplomacy skills checks and Suggestion spells. When the chips are down, buff yourself with Invisibility and Sanctuary and wander the battlefield safely dispensing heals and casting summons -- if you go the Summoner route as a major theme, consider branching into Thaumaturgist. Have effective attack spells at the ready -- Still Magic Missiles and Blindness spells are good for that.
Pick magic items that address your weaknesses. Your caster level sucks, so get an Ioun Strone to boost caster level by +1 ... that boosts BOTH arcane and divine. A Bead of Karma (+4 caster levels for ten minutes) is also sweet, especially if you can talk your DM into letting it boost arcane casting as well. A Candle of Invocation is invaluable if your DM lets it boost your arcane side too. Use your Wizard scroll scribing feat to make cleric and wizard scrolls ... remember that you can put more than one spell on a scroll.
Capitalize on your strengths. Your familiar can deliver cure spells to friends, and so can that Spectral Hand. If you go for the Arcane Tank, take War Domain and a martial weapon you can throw, like light hammer or trident. Get a couple +1 spell storing versions of those (returning spell storing versions maybe) and load them up with Inflict Serious Wounds spells. Cast your True Strike and throw!
You'll never be a good undead turner, so try to use your Turn Undead uses for other things. Find or make a magic item that uses it. Or find or create a feat that lets you use it for something.
What the Heck Do I Know!
Yup, that's all just my opinion. So here -- take a look at what a few other people are saying around the Web: