How can google know that you paid to be in a directory...
In some cases it can probably "guess" which is a paid directory and which isn't. Some directories have their rates on the submit page, so it is more of a no-brainer for google.
Some paid directories still have value.
Paying to be in a Chamber of Commerce directory, or better business bureau directory, or other such "trusted" directory will *probably* count in google's eyes (especially as google is looking for more branding signals from sites).
There is debate as to whether being in yahoo directory or best of the web or some of the other long established paid directories has any SEO value.