I really should know this off by heart (this is my field...) but I never really grasped the difference between the total wavefunction of a system and the wavefunctions of particles within it, so it only just dawned on me that perhaps the total energy of a system was simply the sum of the energies of the individual particles. 

It's true, isn't it?

By 'energy' here, I really mean $\langle E \rangle$. So would the expectation value of the total energy equal the sum of the expectation values of all the component particles? Or is there some conditionality to it? I.e. in a quantum computer, if the states of two qubits are opposites, then the expectation value of the total energy would be the sum of the component energies for each possible scenario $|0\rangle|1\rangle$ and $|1\rangle|0\rangle$, multiplied by the probability of each. 

Took me a long time to learn to ask the stupid questions.

[Edit: brief mathsing for two qubits:

$ \hat{H} \Psi = E \Psi $

$ \Psi = \psi\_m \psi\_n $

$ \psi\_m = a\_m |0\rangle + b\_m |1\rangle \quad\quad\mathrm{(ditto}~~\psi\_n \mathrm{)} $

$ \Psi = a\_m a\_n |0\rangle |0\rangle + a\_m b\_n |0\rangle |1\rangle \dots $

$ \langle E \rangle = a\_m a\_n E\_{00} + a\_m b\_n E\_{01} \dots $ 

or time-independently

$ \langle E(t) \rangle = a\_m(t) a\_n(t) E\_{00}(t) + a\_m(t) b\_n(t) E\_{01}(t) $ ]