I feel like this is a silly question, but I'm a bit uneasy about it so I figured I'd ask anyways...
I have some intricate LED devices (eg an RGB LED pen, for long-exposure light drawing) with built in resistors chosen for a 5v source. I'd like to be able to use these with a 3.3v Arduino clone. Assuming I have a 5v source available, is there any problem with sinking the LEDs into a 3.3v device?
I'm not sure this will work for your purpose and depending on the voltage drop of your leds, it might burn your arduino. The Atmega `68 IO pins are rated for Vcc + 0.5 = 3.3+.5=3.8
You would be better off using an NPN transistor switching circuit with you arduino switching the base.
Assuming I have a 5v source available, is there any problem with sinking the LEDs into a 3.3v device?
To answer the question directly, yes there is a problem. It is that the output pin when off will be exposed to 5V. This is greater than the 3V3 of the supply and so will cause damage.