If you're deploying to a subdirectory on your site, or if you're using Github's project pages, make sure you set up your urls correctly in your configs.
You can do this *almost* automatically:
``` sh
rake set_root_dir[your/path]
# To go back to publishing to the document root
rake set_root_dir[/]
```
Then update your `_config.yml` and `Rakefile` as follows:
``` sh
# _config.yml
url: http://yoursite.com/your/path
# Rakefile (if deploying with rsync)
document_root = "~/yoursite.com/your/path"
```
To manually configure deployment to a subdirectory, you'll change `_config.yml`, `config.rb` and `Rakefile`.