I have never completely understood the justification of this step in the derivation of the E-L equation:
$\delta L = L(q + \delta q, q' + \delta q', x) - L(q, q', x) = \partial_q L \delta q + \partial_{q'} L \delta q'$
This is only valid when both $\delta q$ and $\delta q'$ are small. Now $\delta q$ is small by assumption, but $\delta q'$ is completely determined by $\delta q$, so the smallness of $\delta q'$ needs to be implied by the smallness of $\delta q$. However, if $\delta q$ has high frequency components (eq $\delta q = \epsilon sin(x/\epsilon)$ for a small $\epsilon$) then $\delta q'$ will not be small even though $\delta q$ is. I imagine this can be fixed by having additional assumtions on $\delta q$ like that it is of the form $\epsilon f$ where $\epsilon$ is small and $f$ is just a suitably nice function, but the explanations I have seen do not make such assumptions explicit.
Also I have never seen a good explanation of the properties $\delta$ operator. In the usual E-L derivation it also seems to be assumed that $\delta (q') = (\delta q)'$. I can convince myself of that informally, but it is something that would seem worth explaining. Is there a good reference that goes into the $\delta$ operator in some depth.
EDIT
When I first asked my question I was forgetting about Lanczos Variational Principles of Mechanics which goes into the $\delta$ notation in some length. Now that I have gone back to Lanczos, I know a little bit more, but it is still far from clear, despite Lanczos's heroic efforts.
The responses seem to agree on the idea that $\delta$ is not an independent entity, but more of a naming convention, making $\delta L$ and $\delta q$ atomic names. This makes some sense to me, but it contradicts Lanczos in Variational Principles of Mechanics, where he uses the term $\delta$-process. He even writes things like $\delta^2 F$ and $\delta \int F$ and even has the equivalent of $\delta (q') = (\delta q)'$ above as equation 29.3, together with a derivation. Lanczos stresses the notion of virtual displacement . At one point he says that $\delta u$ is a virtual change while $du$ is an actual change. Unfortunately I have no clue what he is getting at, but virtual displacement seems to be the concept I am missing. I have found http://en.wikipedia.org/wiki/Virtual_displacement, but I am not really parsing that either. However, the abstract of Subhankar Ray, J. Shamanna, Virtual Displacement in Lagrangian Dynamics sounds promising:
... However, the definition of virtual displacement is rarely made precise and often seems vague and ambiguous to students. In this article we attempt a more systematic and precise definition, which not only gives one a qualitative idea of virtual displacement, but also allows one to quantitatively express the same for any given constrained system. ...
Sounds like what the doctor ordered.