I think we need more details here. What do you mean by Smart? If you simply need a local BLAST server where you can customize the databases and still provide a nice web-based UI, you should look at the SequenceServer project.
I'm still trying to understand what exactly you are looking for - it seems like you are suggesting that you want an automated way of deciding which hit in a BLAST search result set is "best"? Or am I misunderstanding you?