Unpacking the manual twice, just to find out wherher it's utf8 -- Bad.
Launching awk per file instead of per dir -- Bad.
Determining which decompressor to use twice -- Bad.
Constantly sorting the database keeping it inconsistent -- Bad.

diff -up man-1.6f/src/makewhatis.sh.perf man-1.6f/src/makewhatis.sh
--- man-1.6f/src/makewhatis.sh.perf	2009-04-19 23:02:45.673198925 +0200
+++ man-1.6f/src/makewhatis.sh	2009-04-19 23:02:45.691198800 +0200
@@ -36,6 +36,8 @@
 # 060719 - section choosing behavior to match man's (Mike frysinger).
 #
 # 090419 - Add -U flag, Lubomir Rintel <lkundrak@v3.sk>
+# 090419 - Don't write the database until we're finished, Lubomir Rintel <lkundrak@v3.sk>
+# 090419 - Substantial performance improvements, Lubomir Rintel <lkundrak@v3.sk>
 #
 # Note for Slackware users: "makewhatis -v -w -c" will work.
 #
@@ -218,24 +220,7 @@ do
 	    cd ${pages}$i
 	    section=$i
 	    curdir=$mandir/${pages}$i
-	    export section verbose curdir
-
-	   utf8=
-            for x in $(find $mandir/${pages}$i -name '*' $findarg0 $findarg)
-            do
-               if [ "${x%.gz}" != "${x}" ]
-               then
-                  cat=zcat
-               elif [ "${x%.bz2}" != "${x}" ]
-               then
-                  cat=bzcat
-               else
-                  cat=cat
-               fi
-   
-               if ${cat} ${x} | iconv -f utf-8 -t utf-8 -o /dev/null 2>/dev/null
-               then
-                  echo ${x} | $AWK '
+            find $mandir/${pages}$i -name '*' $findarg0 $findarg | $AWK '
 
 	    function readline() {
               if (use_zcat || use_bzcat || use_lzcat) {
@@ -295,6 +280,8 @@ do
                 } else {
                   pipe_cmd = "lzcat \"" filename "\" 2>/dev/null";
                 }
+                # Chuck output unless it is utf-8
+                pipe_cmd = pipe_cmd " |iconv -f utf-8 -t utf-8 2>/dev/null"
 		# try to avoid suspicious stuff
 		if (filename ~ /[;&|`$(]/) {
 		  print "ignored strange file name " filename " in " curdir > "/dev/stderr";
@@ -442,24 +429,23 @@ do
 	      do_one();
 	    }
 	    ' pages=$pages section=$section verbose=$verbose curdir=$curdir
-		fi
-	      done
 	    cd ..
 	 fi
-       done > $TMPFILE
+       done >> $TMPFILE
 
        cd "$here"
 
-       if [ -f ${whatisdb} ]
-       then
-         cat ${whatisdb} >> $TMPFILE
-       fi
-       tr -s '\n' < $TMPFILE | sort -u > ${whatisdb}
-
-       chmod 644 ${whatisdb}
    done
+
 done
 
+if [ -f ${whatisdb} ]
+then
+  cat ${whatisdb} >> $TMPFILE
+fi
+tr -s '\n' < $TMPFILE | sort -u > ${whatisdb}
+chmod 644 ${whatisdb}
+
 # remove tempdir
 rm -rf $TMPFILE