I was able to fix my server to check the REQUEST_URI for ikiwiki.cgi and to continue processing if it was not found, passing $ENV{SEVER_NAME} . $ENV{REQUEST_URI} as the first parameter to cgi_page_from_404. However, my perl is terrible and I just made it work rather than figuring out exactly what to do to get it to work on both lighttpd and apache.
This is with lighttpd 1.4.19 on Debian.
+
+> /cgi-bin/ikiwiki.cgi?do=goto also provides redirection in the same way,
+> if that's any help? You might need to set the lighttpd 404 handler to
+> that, then compose REDIRECT_URL from other variables if necessary.
+>
+> I originally wrote the plugin for Apache; [[weakish]] contributed the
+> lighttpd docs and might know more about how to make it work there.
+> --[[smcv]]
+
+>> As I said, I got it working for me, but somebody who knows perl should probably look at it with the aim of making it work for everyone.
+>> I considered having lighttpd construct a proper url for the 404 redirect itself, but I don't know if it can do something like that or not.
+>> For what it's worth, here's the change I made to the module:
+
+ sub cgi ($) {
+ my $cgi=shift;
+ if ($ENV{REQUEST_URI} !~ /ikiwiki\.cgi/) {
+ my $page = cgi_page_from_404(
+ Encode::decode_utf8($ENV{SERVER_NAME} . $ENV{REQUEST_URI}),
+ $config{url}, $config{usedirs});
+ IkiWiki::Plugin::goto::cgi_goto($cgi, $page);
+ }
+
+ # if (exists $ENV{REDIRECT_STATUS} &&
+ # $ENV{REDIRECT_STATUS} eq '404') {
+ # my $page = cgi_page_from_404(
+ # Encode::decode_utf8($ENV{REDIRECT_URL}),
+ # $config{url}, $config{usedirs});
+ # IkiWiki::Plugin::goto::cgi_goto($cgi, $page);
+ # }
+ }