The way I've seen it done most often is in an XML document with CDATA tags:
m44 vt0, va0, vc0
mov v0, va1
mov v1, va2
mov op, vt0
tex ft0, v1, fs0 <2d,repeat,linear,nomip>
mov oc, ft0
You can embed it like any other asset (as Flashpunk does with the default font already) and get the shader text from it when the engine starts up.