Here are the rules that you need to add to a server configuration for Nginx to operate as a WebPagetest server.  Make sure to change the script path in the fcgi section.

        location / {
                index  index.php;
        }

        # disable chunked encoding for mp4 files because it breaks flash video on firefox
        location ~* \.mp4 {
                gzip off;
        }

        # deny access to .htaccess files, if Apache's document root
        # concurs with nginx's one
        location ~ /\.ht {
                deny  all;
        }

        # block protected files
        location ~* \.(gz|ini|inc) {
                deny all;
        }

        #webpagetest rewrite rules
        rewrite ^/about$ /about.php last;
        rewrite ^/traceroute$ /traceroute.php last;
        rewrite ^/mobile$ /mobile.php last;
        rewrite ^/tips$ /tips.php last;
        rewrite ^/pss$ /pss.php last;
        rewrite ^/compare$ /pss.php last;
        rewrite ^/blink$ /blink.php last;

        #result paths
        rewrite ^/result/([a-zA-Z0-9_]+)$ /result/$1/ permanent;
        rewrite ^/result/([a-zA-Z0-9_]+)/$ /results.php?test=$1 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/waterfall$ /result/$1/$2/details/ permanent;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/waterfall/$ /result/$1/$2/details/ permanent;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/details/$ /details.php?test=$1&run=$2  last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/waterfall/cached$ /result/$1/$2/details/cached/ permanent;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/waterfall/cached/$ /result/$1/$2/details/cached/ permanent;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/details/cached/$ /details.php?test=$1&run=$2&cached=1  last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/optimization$ /result/$1/$2/performance_optimization/ permanent;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/optimization/$ /result/$1/$2/performance_optimization/ permanent;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/performance_optimization/$ /performance_optimization.php?test=$1&run=$2  last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/optimization/cached$ /result/$1/$2/performance_optimization/cached/ permanent;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/optimization/cached/$ /result/$1/$2/performance_optimization/cached/ permanent;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/performance_optimization/cached/$ /performance_optimization.php?test=$1&run=$2&cached=1 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/screen_shot/$ /screen_shot.php?test=$1&run=$2 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/screen_shot/cached/$ /screen_shot.php?test=$1&run=$2&cached=1 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/breakdown/$ /breakdown.php?test=$1&run=$2 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/breakdown/cached/$ /breakdown.php?test=$1&run=$2&cached=1 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/domains/$ /domains.php?test=$1&run=$2 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/domains/cached/$ /domains.php?test=$1&run=$2&cached=1 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/optimization_report/$ /optimization_report.php?test=$1&run=$2 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/optimization_report/cached/$ /optimization_report.php?test=$1&run=$2&cached=1 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/pagespeed/$ /pagespeed.php?test=$1&run=$2 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)/pagespeed/cached/$ /pagespeed.php?test=$1&run=$2&cached=1 last;
        rewrite ^/testlog/([0-9]+)$ /testlog/$1/ permanent;
        rewrite ^/testlog/([0-9]+)/$ /testlog.php?days=$1 last;
        rewrite ^/xmlResult/([a-zA-Z0-9_]+)/$ /xmlResult.php?test=$1 last;
        rewrite ^/testlog.csv /testlog.php?f=csv last;
        rewrite ^/waterfall.png /waterfall.php last;

        #old direct path to images
        rewrite ^/results/([a-zA-Z0-9])([a-zA-Z0-9]+)/([a-zA-Z0-9_]+).png$ /results/old/_$1/$1$2/$3.png last;
        rewrite ^/results/([a-zA-Z0-9])([a-zA-Z0-9]+)/([a-zA-Z0-9_]+).jpg$ /results/old/_$1/$1$2/$3.jpg last;
        rewrite ^/results/old/_([a-zA-Z0-9])/([a-zA-Z0-9]+)/([a-zA-Z0-9_]+).png$ /results/old/$2/$3.png last;

        #csv combined results
        rewrite ^/result/([a-zA-Z0-9_]+)/.*page_data.csv$ /csv.php?test=$1 last;
        rewrite ^/result/([a-zA-Z0-9_]+)/.*requests.csv$ /csv.php?test=$1&requests=1 last;

        #thumbnails
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)_screen_thumb.jpg$ /thumbnail.php?test=$1&run=$2&file=$2_screen.jpg last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)_Cached_screen_thumb.jpg$ /thumbnail.php?test=$1&run=$2&cached=1&file=$2_Cached_screen.jpg last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)_waterfall_thumb.png$ /thumbnail.php?test=$1&run=$2&file=$2_waterfall.png last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)_Cached_waterfall_thumb.png$ /thumbnail.php?test=$1&run=$2&cached=1&file=$2_Cached_waterfall.png last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)_optimization_thumb.png$ /thumbnail.php?test=$1&run=$2&file=$2_optimization.png last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)_Cached_optimization_thumb.png$ /thumbnail.php?test=$1&run=$2&cached=1&file=$2_Cached_optimization.png last;

        #old direct thumbnail paths
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_screen_thumb.jpg$ /thumbnail.php?test=$1&run=$2&file=$2_screen.jpg last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_Cached_screen_thumb.jpg$ /thumbnail.php?test=$1&run=$2&cached=1&file=$2_Cached_screen.jpg last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_waterfall_thumb.png$ /thumbnail.php?test=$1&run=$2&file=$2_waterfall.png last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_Cached_waterfall_thumb.png$ /thumbnail.php?test=$1&run=$2&cached=1&file=$2_Cached_waterfall.png last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_optimization_thumb.png$ /thumbnail.php?test=$1&run=$2&file=$2_optimization.png last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_Cached_optimization_thumb.png$ /thumbnail.php?test=$1&run=$2&cached=1&file=$2_Cached_optimization.png last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_waterfall_thumb.gif$ /thumbnail.php?test=$1&run=$2&file=$2_waterfall.gif last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_Cached_waterfall_thumb.gif$ /thumbnail.php?test=$1&run=$2&cached=1&file=$2_Cached_waterfall.gif last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_optimization_thumb.gif$ /thumbnail.php?test=$1&run=$2&file=$2_optimization.gif last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_Cached_optimization_thumb.gif$ /thumbnail.php?test=$1&run=$2&cached=1&file=$2_Cached_optimization.gif last;

        # waterfalls
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_waterfall.png$ /waterfall.php?test=$1&run=$2 last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_Cached_waterfall.png$ /waterfall.php?test=$1&run=$2&cached=1 last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_waterfall.gif$ /waterfall.php?test=$1&run=$2 last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_Cached_waterfall.gif$ /waterfall.php?test=$1&run=$2&cached=1 last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([0-9]+)_waterfall.png$ /waterfall.php?test=$1$2$3_$4&run=$5 last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([a-zA-Z0-9_]+)/([0-9]+)_waterfall.png$ /waterfall.php?test=$1$2$3_$4_$5&run=$6 last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([0-9]+)_Cached_waterfall.png$ /waterfall.php?test=$1$2$3_$4&run=$5&cached=1 last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([a-zA-Z0-9_]+)/([0-9]+)_Cached_waterfall.png$ /waterfall.php?test=$1$2$3_$4_$5&run=$6&cached=1 last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([0-9]+)_connection.png$ /waterfall.php?test=$1$2$3_$4&run=$5&type=connection last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([a-zA-Z0-9_]+)/([0-9]+)_connection.png$ /waterfall.php?test=$1$2$3_$4_$5&run=$6&type=connection last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([0-9]+)_Cached_connection.png$ /waterfall.php?test=$1$2$3_$4&run=$5&cached=1&type=connection last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([a-zA-Z0-9_]+)/([0-9]+)_Cached_connection.png$ /waterfall.php?test=$1$2$3_$4_$5&run=$6&cached=1&type=connection last;

        # optimization checklists
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_optimization.png$ /optimizationChecklist.php?test=$1&run=$2 last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_Cached_optimization.png$ /optimizationChecklist.php?test=$1&run=$2&cached=1 last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_optimization.gif$ /optimizationChecklist.php?test=$1&run=$2 last;
        rewrite ^/results/old/([a-zA-Z0-9_]+)/([0-9]+)_Cached_optimization.gif$ /optimizationChecklist.php?test=$1&run=$2&cached=1 last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([0-9]+)_optimization.png$ /optimizationChecklist.php?test=$1$2$3_$4&run=$5 last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([a-zA-Z0-9_]+)/([0-9]+)_optimization.png$ /optimizationChecklist.php?test=$1$2$3_$4_$5&run=$6 last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([0-9]+)_Cached_optimization.png$ /optimizationChecklist.php?test=$1$2$3_$4&run=$5&cached=1 last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([a-zA-Z0-9_]+)/([0-9]+)_Cached_optimization.png$ /optimizationChecklist.php?test=$1$2$3_$4_$5&run=$6&cached=1 last;

        #location cookie dropping
        rewrite ^/loc/([a-zA-Z0-9_]+)$ /util/setloc.php?location=$1 last;
        rewrite ^/loc/([a-zA-Z0-9_]+)$/ /util/setloc.php?location=$1 last;

        #gzip compressed text result files
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([a-zA-Z0-9_]+).(txt|csv)$ /gettext.php?test=$1$2$3_$4&file=$5.$6 last;
        rewrite ^/results/([0-9][0-9])/([0-9][0-9])/([0-9][0-9])/([a-zA-Z0-9_]+)/([a-zA-Z0-9_]+)/([a-zA-Z0-9_]+).(txt|csv)$ /gettext.php?test=$1$2$3_$4_$5&file=$6.$7 last;

        #tcpdump capture files
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+).cap$ /getgzip.php?test=$1&file=$2.cap last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)_Cached.cap$ /getgzip.php?test=$1&file=$2_Cached.cap last;

        #page speed
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)_pagespeed.txt$ /getgzip.php?test=$1&file=$2_pagespeed.txt last;
        rewrite ^/result/([a-zA-Z0-9_]+)/([0-9]+)_Cached_pagespeed.txt$ /getgzip.php?test=$1&file=$2_Cached_pagespeed.txt last;

        #embeddable video widget
        rewrite ^/video/embed/([a-zA-Z0-9_]+)$ /video/view.php?embed=1&id=$1 last;
        
        #widgets
        rewrite ^/widgets/pagespeed/tree$ /widgets/pagespeed/tree.php last;

        #old pages that were eliminated in the UI rewrite
        rewrite ^/test$ / permanent;

        #wiki
        rewrite ^/docs/(.*)$ http://www.webperformancecentral.com/wiki/WebPagetest/$1 permanent;
        rewrite ^/docs$ http://www.webperformancecentral.com/wiki/WebPagetest permanent;

        # pass the PHP scripts to FastCGI server listening on 127.0.0.1:9000
        #
        location ~ \.php$ {
                fastcgi_pass   127.0.0.1:9000;
                #fastcgi_index  index.php;
                fastcgi_param  SCRIPT_FILENAME  /var/www/webpagetest.org$fastcgi_script_name;
                fastcgi_param  HTTP_MOD_REWRITE On;
                include fastcgi_params;
        }

        # static files
        location ~* \.(js|css|png|jpg|jpeg|gif|ico)$ {
            expires max;
            log_not_found off;
        }