RewriteRule responds to any URL request and unless it examines the HTTP_REFERER variable has no idea where that click came from.
The following rule matches the pretty URL request and internally rewrites the pointer to point at the actual internal filepath inside the server filesystem that will deliver the content:
RewriteRule ^emulators/atari/800$ /emulators/index.php?folder=atari/800 [L]
In real life the rule pattern would contain a regular expression to match URLs all having the same pattern and the rule target would contain backreferences re-using those values.
RewriteRule ^emulators/(([^/]+/)*[^/.]+)$ /emulators/index.php?folder=$1 [L]
Your requested page URL must NOT end with a trailing slash (be aware that in your examples one did and one did not - attention to this small detail is the crucial difference between success and failure).