Ethan Marcotte documented his workflow for storing GIFs in a web directory. Sometimes just SFTPing files into a folder is as fancy a workflow as you need, and in fact, modern workflows don’t have anything on it!
I’ve also used Transmit’s fancy features for this kind of thing. I prefer saving the connection as a Droplet, which is basically a little application you can drop a file onto and have it upload to exactly where you want it…say a GIF in a specific server directory.
There are two things that make this even more useful. One, you can have it copy the URL after uploading:
Two, you can set rules for file types so that they have the right permissions as soon as they are uploaded. I find this particularly useful for S3 where by default they aren’t “world readable” and need to be changed manually. This rule prevents that from being a manual step every time.