Caster level refers to caster level in one spellcasting class.
Feat prerequisites are primarily defined as referring to "a class level", not total character level or some combination of class levels. Player's Handbook, p.89, Feat Name, states:
Prerequisite: A minimum ability score, another feat or feats, a minimum base attack bonus, a minimum number of ranks in one or more skills, or a class level that the character must have in order to acquire this feat.
It's possible to assert some ambiguity here: Player's Handbook p.87 allows for qualities other than those listed above, Leadership (originally limited to the Dungeon Master's Guide in 3.0) uses total character level as a prerequisite, and "caster level" for the specific purpose of meeting item creation prerequisites is not explicitly defined.
However, the rules for interpreting ambiguous situations in D&D 3.5 are clear.
As per the D&D 3.5 Dungeon Master's Guide. p.6, Adjudicating, situations not explicitly covered by the rules should be adjudicated based on inferences from similar rules:
Loop to any similar situation that is covered in the rulebook. Try to extrapolate from what you see presented there and apply it to the current circumstance.
Caster level in the context of spellcasting always refers to your caster level a single class, not your total class levels. Player's Handbook p.171, Caster Level, states:
A spell's power often depends on its caster level, which for most spellcasting characters is equal to your class level in the class you're using to cast the spell.
Caster level in the context of magic item caster level for items which replicate a spell always refers to the level in one class, not total classes. Player's Handbook p.88, Item Cost states:
Brew Potion, Craft Wand, and Scribe Scroll create items that directly reproduce spell effects, and the power of these items depends on their caster level—that is, a spell from such an item has the power it would if cast by a spellcaster of that level.
In fact, with the exceptions of unique abilities of certain prestige classes and any mechanics based on total character level, there's no D&D game mechanic in the core rules which allows you to add together levels in multiple casting classes to determine caster level.
The D&D 3.5 FAQ, p.30, notes that caster level can be increased with feats and temporary effects, implying that the Practiced Spellcaster feat would allow a Wiz9/Sor3 to have an effective caster level of 12. Complete Arcane, p.82, gives a similar example which concurs:
For example, a human 5th-level sorcerer/3rd-level fighter who selects this feat would increase his sorcerer caster level from 5th to 8th (since he has 8 Hit Dice).