I think there is nothing wrong with running few paster instances, but you should consider using FastCGI (or wsgi) and Virtual Hosts, because it's more suitable for "production environment". 
Example with FastCGI:
pid         /var/run/nginx.pid;
user            www;
worker_processes    1;
events {
    worker_connections  1024;
}
http {
    include     /etc/mime.types;
    default_type    application/octet-stream;
    sendfile        on;
    gzip            on;
    keepalive_timeout   65;
    # First site
    server {
        listen *:443;
        server_name     first.example.com;
        ssl         on;
        ssl_certificate     /etc/www/cert.pem;
        ssl_certificate_key /etc/www/key.pem;
        ssl_session_timeout 5m;
        ssl_protocols       SSLv3 TLSv1;
        location / {
            fastcgi_pass            127.0.0.1:9000;
            fastcgi_param PATH_INFO     $fastcgi_script_name;
            fastcgi_param REQUEST_METHOD    $request_method;
            fastcgi_param QUERY_STRING  $query_string;
            fastcgi_param CONTENT_TYPE  $content_type;
            fastcgi_param CONTENT_LENGTH    $content_length;
            fastcgi_param REMOTE_ADDR   $remote_addr;
            fastcgi_param SERVER_ADDR   $server_addr;
            fastcgi_param SERVER_PORT   $server_port;
            fastcgi_param SERVER_NAME   $server_name;
            fastcgi_param SERVER_PROTOCOL   $server_protocol;
            fastcgi_param HTTPS     on;
            fastcgi_pass_header     Authorization;
            fastcgi_intercept_errors    off;
        }
        access_log  /var/log/first.access.log main;
        error_log   /var/log/first.error.log;
    }
    # Second site
    server {
        listen *:443;
        server_name     second.example.com;
        ssl            on;
        ssl_certificate        /etc/www/cert1.pem;
        ssl_certificate_key    /etc/www/key1.pem;
        ssl_session_timeout    5m;
        ssl_protocols        SSLv3 TLSv1;
        location / {
            fastcgi_pass            127.0.0.1:9001;
            fastcgi_param PATH_INFO        $fastcgi_script_name;
            fastcgi_param REQUEST_METHOD    $request_method;
            fastcgi_param QUERY_STRING    $query_string;
            fastcgi_param CONTENT_TYPE    $content_type;
            fastcgi_param CONTENT_LENGTH    $content_length;
            fastcgi_param REMOTE_ADDR    $remote_addr;
            fastcgi_param SERVER_ADDR    $server_addr;
            fastcgi_param SERVER_PORT    $server_port;
            fastcgi_param SERVER_NAME    $server_name;
            fastcgi_param SERVER_PROTOCOL    $server_protocol;
            fastcgi_param HTTPS        on;
            fastcgi_pass_header        Authorization;
            fastcgi_intercept_errors    off;
        }
        access_log    /var/log/second.access.log main;
        error_log    /var/log/second.error.log;
    }
}
Now, you have to sites:
first.example.com -> localhost:9000
second.example.com -> localhost:9001
You can also set IP in for "listen", e.g.:
listen 192.168.1.1:443;
listen 192.168.1.2:443;
so you are able to use IP instead of DNS name.
For Pylons app you should change configuration to FastCGI:
[server:main]
use = egg:Flup#fcgi_thread
host = 127.0.0.1
port = 9000
for first host, and for second:
[server:main]
use = egg:Flup#fcgi_thread
host = 127.0.0.1
port = 9001
Hope this helps.