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
You have two “types” of level: character level and class level
Your class level is, as the name may imply, your level in any one class. So if you’ve chosen the Wizard class five times on level-up, you have a Wizard class level of 5.
Your character level is the sum total of your class levels. If, in addition to those five level-ups where you chose Wizard, you’d started as a Rogue and leveled-up as a Rogue once (Rogue class level 2), your character level is 7.
There are also Racial Hit Dice and Level Adjustment in 3.5; these count towards character level and are not class levels, but honestly there are very few cases where I can recommend taking either so I’m not going to spend any more time on them. The RHD/LA system was not the most well thought-out ones in the books.
So when you talk about “my level” what you really mean is your character level. This is what determines how much XP you need to level up next time, it determines your maximum rank in skills, it determines whether or not you are affected by spells like sleep, and so on.
Note that every time you level up, you gain a Hit Die; your number of Hit Dice is therefore equal to your character level (excepting LA which we’re not getting into here), so if you see something that needs x HD (like being immune to sleep), it means you need a character level of at least x.
Multiclassing
When you multiclass, it means that instead of taking the next level of whatever class you were in, you instead take the first level in some other class. So back when you were character level 2, having started as a Rogue and leveled-up once, you could decide to take Wizard 1 instead of Rogue 3. This means that you have all the features of a Rogue 2 (Sneak Attack +1d6, Trapfinding, Evasion, etc.), and all of the class features of a Wizard 1 (some spells, a Familiar, Scribe Scroll, and a spellbook).
Your character level is still 3, which means, among other things, that you have 3 HD (two d6s from your Rogue levels and one d4 from your Wizard level), your maximum skill rank is 6 (3+HD), and you need 10,000 XP to level-up to character level 4.
If you continue to choose Wizard for four more additional levels, as above, you are a Rogue 2/Wizard 5 (character level 7), and still have the same class features of a Rogue 2, while having the class features of a Wizard 5 (more and higher-level spells, plus a Bonus Feat). Continuing to level Wizard means your Rogue features do not advance: you do not gain more Sneak Attack damage, Improved Evasion, and so on. This is why prestige classes like Arcane Trickster exist: they can advance both.