in reply to alphabetize a hash ignoring upper/lower cases

Just compare the lowercase/uppercase variants of the strings. Make sure you convert all of them to common case (using the lc or uc methods). For example, I'd try a code like this:
foreach $orf (sort {lc($mips{$a}) cmp lc($mips{$b})} keys %mips) { push @mips, $mips{$orf}; }
(note: didn't test the code snippet, but confident it should work)

# Under Construction