The 8th-level Sor/Wiz spell clone [necro] (Player's Handbook 210), when used to create a duplicate of a creature that still lives, creates a "body [that] is merely a soulless bit of inert flesh." The Monster Manual says, "Anything that lacks Wisdom or Charisma is an object, not a creature" (298), and this should include inanimate things that were never alive in the first place despite their forms being composed of flesh. Thus the 6th-level Clr spell animate objects [trans] (PH 199) should be able to affect the body. However, ask the DM to confirm this supposition; it's likely the game didn't consider that a caster would be willing to spend 2d4 months growing a duplicate of some dude just to put puppet strings on it!
Also, keep in mind that the spell animate objects only gives only limited control over objects it affects. I mean, seriously, the spell says, "You imbue inanimate objects with mobility and a semblance of life." What does this semblance of life actually allow the affected objects to do? The game says only this: "Each such animated object then immediately attacks whomever or whatever you initially designate" (ibid.). There's no mechanism—except DM largess—for affected objects doing anything but attacking (or, I guess, not attacking) whoever the caster designates. (Presumably, it's the application of the 5th-level Sor/Wiz spell permanency [univ] (PH 259-60) to the objects affected by the animate objects spell that expands animated objects' range of commands obeyed from Attack! to any "orders without question and to the best of their abilities" (Monster Manual 13).)
Further, even if the DM goes along with this complicated, long-range, slightly shady clonepuppet plan (also a good band name), the inert flesh that's the result of the clone spell has no capacity for self-repair and straight-up "rots if not preserved" (PH 210). Finally, add to this that the spell animate objects makes no mention of imparting to affected objects the capacity for speech! Combined, this means any plans to have the animated object infiltrate an organization for an extended period must be made carefully—it could, for instance, probably join an order of pacifist monks. (Yet even they, I'm sure, would eventually wonder about its smell.)
This DM would rule that a flesh golem can't be made from clone parts
The Monster Manual on Construction says
The pieces of a flesh golem must come from normal human corpses that have not decayed significantly. Assembly requires a minimum of six different bodies—one for each limb, the torso (including head), and the brain. (136)
This DM would rule that the products of clone spells are not "normal human corpses," but, instead, that the product of a clone spell is—like the spell's description says—just a "soulless bit of inert flesh." What the wizard's grown in a vat in her laboratory certainly isn't normal, is an object not a human, and will have to be somehow given life then die to become a corpse.
Note: I know that disempowering answers are unpopular, and I hate being the bearer of bad news, so let me offer up by way of recompense one of my favorite plot hooks, the libram of flesh (178,000 gp; 5 lbs.) from Arms and Equipment Guide 134. It enables the user to make from corpses flesh golems that have the special abilities of the bodies from which they're made. It's kind of awesome even if the DM does pick the special abilities.