"If eval() is the answer, you're almost certainly asking the wrong question."
-Rasmus Lerdorf, BDFL of PHP
Is the code you are running so varied that it can't be decided upon as a series of files to be included on demand or a XML-RPC style function call? There is generally very little to gain by allowing arbitrary code execution, and that's before you consider the staggering amount you stand to lose.
If there is a finite, predictable number of things these files could possibly do, I would Strongly recommend taking the time to create a semi-generic XML-RPC interface (or at least a series of files that you could specify in the XML file and then include on-the-fly, perhaps after setting some environment variables, depending on your coding style) and using that.
The number of risks you take when creating a portal to eval()
are nigh innumerable.
I had considered providing some examples here, but XML-RPC ought to be a well enough known concept that my doing so is altogether unnecessary.