The rules don't actually define the terminology except as far as the phrases themselves. To wield a two-handed weapon, you have to use two hands. So your Mordenkrad cannot be wielded while throwing your hammer, since you can't hold it in two hands, and you will not get any associated bonuses if they applied.
I see nothing wrong with merely holding it up while you use the hammer, and I don't know of any associated penalties, since the rules don't cover it. It's not much different than throwing with a shield equipped.
Magical thrown weapons automatically return to their owner's hands after the attack is resolved, so if your Dwarven Thrower is magical, you will have to ignore the catch (which per the Rules Compendium you can do) and let it drop to the ground before putting your main hand back on the Mordenkrad.
Thou shalt not sacrifice caster levels.
As the golden rule of 3.5 multiclssing, it's hard to beat the above. It's quite possible to apply requirements gathering methods to 3.5 as well as 4e, and estimate approximate to-hit and damage at each level.
Plan out your character to 20.
To answer:
s there an effective way to identify class combinations which seem appealing up front, but which will fall behind as the characters level up (without actually taking the character through its paces in a game)?
is simple: plan out your character to level 20. Identify, at each level, what benefit the character is deriving from your choices. Test against the requirements given in your requirements step. This way, when your character shows up in game, you have an idea of your intent and the capabilities of the character.
To answer what classes synergize well:
Non primary-casting classes tend to synergize well.
Given that most aspects of a level up are cumulative with prior choices (BAB, feats, HP) you want to avoid class features which depend on your level in the class. Therefore, avoid class features which have level as a variable within the feature.
Rages from barbarian are fine. You get more as you level up:
a barbarian can rage for a number of rounds per day equal to 4 + her Constitution modifier. At each level after 1st, she can rage for 2 additional rounds.
but you don't have the benefits of the rage reduced (proportionally to your compatriots) as you see in spells.
For the casting classes it's certainly possible to combine them in "gishy" characters (spell-slinging fighters) but they require a specific focus into the combination, preferably enabled by appropriate choice of prestige classes.
So, if you fail to raise rogue, you don't get as much sneak attack bonus damage, but if you're increasing fighter as the other class, you get a higher BAB to compensate.
Whereas a rogue would effectively be writing off "improved uncanny dodge" due to multiclassing.
Therefore, a good combination can be fighter/rogue, because each class brings a separate thing to the table, without having a significant opportunity cost for choosing the other. Other good combinations are those that lead up to exceptional PrCs, which combine features from both classes in useful synergy.
Best Answer
Throwing is notable for basically one thing: it can be both dual-wielding and ranged. And those combat styles share a common element: they focus on a large number of attacks. The thing about throwing is that it can, in theory, be both at once and get all the attacks.
This commonality actually goes a bit deeper: both of these combat styles get all these attacks through feats. Archery typically uses 6-7 feats.1 Dual-wielders need at least 3.2 Throwing itself often adds in 1 or 2 more.3 In a game where you only get 10 by default, and those slowly over the long course of the game, and several of them are burned on useless feats you need to get the real feats later, that is an untenable situation.
Thus, a good thrower is always going to have to involve bonus feats. Neither knife master nor hurler get any. If you use either, it will have to be done with some judicious multiclassing, but note that Pathfinder punishes multiclass characters extremely harshly.
The most efficient way to get bonus feats, of course, is with fighter. Fighter also improves your accuracy, particularly over the knife master, which is good because many of these feats involve attack penalties.
There are, kind of surprisingly, no fighter archetypes focusing on thrown weapons, though the two-weapon warrior has some benefit for you. Ultimately, though, its effects aren’t that good, and so we default to lore warden just because it’s the best general-case fighter archetype.
How much fighter to take is a question, but since you’re here for bonus feats, stopping after just 2 is very valid. Otherwise, it’s mostly a question of how much you want feats sooner rather than later. If you go in for the long haul, the hair’s breadth and swift lore features of the lore warden are pretty good, as is your first weapon mastery.
If you multiclass, barbarian is better than rogue; it has higher accuracy and it is less reliant on conditional bonuses. Sneak attack can be very difficult to apply at range. Hurler is nice enough, particularly with thrown weapons that often have very limited ranges, and it’s super lightweight which maintains compatibility with other archetypes. Elemental Kin is another ultra lightweight archetype that can extend your daily use of rage—very valuable when you’ve given up a fair amount of rage due to your fighter levels.
Point-blank Shot, Precise Shot, Deadly Aim, Rapid Shot, Manyshot, and then one or more of Clustered Shot, Hammer the Gap, or Improved Precise Shot.
Two-Weapon Fighting, Improved Two-Weapon Fighting, and Greater Two-Weapon Fighting. Ultimately, the large penalties on iteratives make these less valuable, however, so you could live without GTWF or even ITWF.
Quick Draw and possibly Far Shot, though items, particularly blinkback belt, help avoid these.