What is the most common and updated database? - (Nov/16/2012 )
You probably need to look for the Refseq - which is the curated form and the "definitive" version. You can also see the date of upload on the entry, but I don't know how to find the most recent.
As far as I know human sequences for example were all merged recently into one reference sequence for each chromosome, so there is no more multiple contigs. But since more than thousand human genomes have been completely sequence by now, the question of what sequence is actually reference wil probably appear in future, but that would be really mostly a matter of SNPs only.
As bob1 said, when blasting human or mouse select Genomic+transcript database, which should contain reference sequences only, and for any other choose refseq database, maybe limit it by a species you work with in the field below (if you don't want to blast across species of course).