example.com/store/my-funny-test-product.html or example.com/store/city/my-funny-test-product.html

example.com/store/index.php/my-funny-test-product.html or example.com/store/index.php/city/my-funny-test-product.html

location ~ ^/store/(.*) {
rewrite ^/store/(.*)$ /store/index.php$1;
}

2014/11/22 [notice] 9611#0: *816 "^/store/(.*)$" matches "/store/index.phpindex.phpmy-funny-test-product.html", client: xxxx, server: xxx, request: "GET /store/my-funny-test-product.html?token=1234 HTTP/1.1", host: "xxxx"

## The whole setup stays close with the magento recommendations
    ## http://www.magentocommerce.com/wiki/1_-_installation_and_configuration/configuring_nginx_for_magento

server {
    listen myip:80;
    server_name .example.com;

    root /var/www/mydomain/public_html;

    location / {
        index index.html index.php;
        try_files $uri $uri/ @handler;
    }

    ## here comes my rewrite stuff to remove index.php from the subfolder ##
    location ~ ^/store/(.*) {
    rewrite ^/store/(.*)$ /store/index.php$1;
    }

    ## followed by some deny rulesets not relevant here ##

    location @handler { ## Magento common front handler
        rewrite / /index.php;
    }

    location ~ .php/ { ## Forward paths like /js/index.php/x.js to relevant handler
        rewrite ^(.*.php)/ $1 last;
    }

    location ~ .php$ { ## Execute PHP scripts
        if (!-e $request_filename) { rewrite / /index.php last; } ## Catch 404s that try_files miss

        expires        off; ## Do not cache dynamic content
        fastcgi_pass   127.0.0.1:9000;
        fastcgi_param  HTTPS $fastcgi_https;
        fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
        fastcgi_param  MAGE_RUN_CODE default; ## Store code is defined in administration > Configuration > Manage Stores
        fastcgi_param  MAGE_RUN_TYPE store;
        include        fastcgi_params; ## See /etc/nginx/fastcgi_params
    }