Clearly for a USB type pen drive the MCU would have to be a USB host to be able to talk to the FLASH device. This is only feasible with a handful of microcontrollers that support host side controller ports. One type to look for would be a controller that supports USB-on-the-GO. Look also into the FTDI latest technology as here:
http://www.vinculum.com/prd_vnc1l.html

Now with the USB issue explained then there is the issue of file system compatibility. For a FLASH device, be it a USB drive or other card like SD card or CF card to be really useful and data portability between a PC and the embedded environment it is necessary to have a file system. That takes a good sized amount of firmware and for any a reasonable speed also requires some K-bytes of RAM for 512 byte block buffers. On an 8051 type MCU I find that file system code could take about 20K of instruction space and the media will be very slow unless you can allocate space for at least 10 to 15 disk blocks.

It really makes most sense to think about connecting PEN drive devices to MCUs that are the bigger brothers to 8051 types.

Michael Karas