I have a site that gets deployed to over a dozen clients. The main website has a base template, and each client has a client folder that overrides the colours. The problem i
Another option to consider may just be to use a "CSS compiler" -- such as SASS, LESS or even HSS which may support handy constructs like "mixins" and including other files. This approach may allow a system that, while not dynamic, is easily configurable to your different client's needs.
For instance, with a "CSS compiler" the entire color schema could be stored in a single file as exportable variables or templates (depends on "compiler") -- modify that file, "recompile"** and wham, new color-scheme interface is everywhere (SASS also supports math on colors -- such as Hue shifting). This may make the deployment/management of using static content feasible enough for your purposes.
I use SASS (it fit my needs/style whereas LESS/HSS did not). I would not switch back unless I really, really had to (which is to say: uhh, never) -- SASS in SCSS mode also understands CSS syntax so you can micro-evolve or mix and match (LESS and HSS also work like this, but HSS only works with a stricter subset of CSS syntax). CSS compilers can also be used in conjunction templates engines (such as TT4) or take advantage of including dynamically generated files (not dynamic-dynamic as in the question, but dynamic in the sense that they come from some other data-source) if extra power is needed.
While just normal CSS cascading and class names/selectors can go a long ways, I find it much easier to separate the "logical cascade" (CSS, where CSS/cascading is vital) and "geeze, I wish this worked like a template" (CSS compiler, which should handle cases where CSS/cascading is abused).
** Both SASS and LESS can monitor files and recompile them automatically for you. SASS even allows monitoring entire directories