I assume you have used blast to align some reads "reads.fa" onto a reference "ref.fa", and have a blast report in "out.bls" ?

% formatdb -i ref.fa -p F
% blastall -p blastn -i reads.fa -d ./ref.fa -o out.bls

As RM answered, you can (hackily) get the read IDs that got no hits. I have added extra code to ensure a clean list of IDs only into "nohits.ids":

% grep -B5 "***** No hits" out.bls | grep '^Query=' | sed 's/^Query= //' > nohits.ids

Now if you want to get back the sequences listed in nohits.ids from reads.fa, you can use this trick:

% formatdb -i reads.fa -p F
% fastacmd -d ./reads.fa -i nohits.ids -D 1 -o nohits.fa

Good luck!