Are you referring to using camera filters or those used during post production? I'm guessing the latter, but making sure! I've had some photos rejected for "overfiltering." They were ones that I thought looked really awesome, but I gather they may lose some usefulness to certain designers!
If the filter is adding / enhancing the expected effect on the viewer, then it is generally accepted. I have some horror shots which are a little desaturated and increased structure. The original was mostly funny, but not creepy for sure :)