IDs are databse specific. Can you tell which database you want to have IDs from (i.e. genbank, ensemble, etc)?

This http://biodb.jp/#ids may be want you want to use, but it does not work right now. Or try playing around with ENSEML biomart http://www.ensembl.org/biomart/martview

Update:

Assume you are working with the Yeast database (because the ID you gave as an example is from here: http://www.yeastgenome.org/locus/S000029654/overview

So do the following:

1. Download this cross reference file from here

2. Put all your genes in a file called mygenes.txt in one column, for example:

   FLP1
   CKS1
   GCN4
   PAP1
   

3. Make sure dbxref.tab and mygenes.txt are in the same folder. Run this (in a linux machine):

   gawk 'BEGIN{FS="\t"}(NR == FNR){a[$1]++;next}{ if ($6 in a) print $4"\t"$6}' mygenes.txt dbxref.tab |sort|uniq