I (probably) have settled on using FastCGI. It's quite a bit faster than the PHP as CGI option(the startup overhead is smaller). I did have to modify an obscene amount of code to get it working decently, though, so I can't really recommend it to anyone else(except maybe extremely high-traffic sites with a dedicated server).
When I did test running PHP as normal CGI, I didn't use suphp. I modified suexec(which I used already) to run slightly differently(no checks for the executable bit, modified execution function call, etc.) when supplied with a filename ending in ".php", and set up Apache to use the cgi_script handler for *.php.