I'm playing a completely unmodded version of Fallout 3, all DLC included, and for the most part it runs without trouble, nit there are a few scattered incidents of what I am assuming are missing meshes (giant red diamonds with exclamation points) including, but not limited to, a "Super Mutant Overlord" in the path to Vault 87 and 2 objects in the Project Purity control room, each directly inside the doorways. If anyone knows the cause of these issues, or better yet, a solution, please let me know.

Which version is the game, Retail Disk Version or Steam?

Where is the game installed? If it is installed in programs folder in Windows Vista and Higher that could be an issue due to UAC and the extra protection that windows uses when running programs there.