There are several significant differences..
All the search processing and indexing is done on boardtracker servers which removes a lot of load from your servers.
There are none of the forced limits that vb search has such the not allowing searches with 3 characters or less, having to wait 30 seconds between searches, etc.
You can if you choose include results from multiple boards in your search - for example if you run several boards you can circulate traffic between them or you can set up traffic trades with other board admins and include each others results in your boards search.
You can also enable 'global search' as an option for your users - this puts a checkbox on the search page so users can perform the search on all boards in boardtracker - why send them to google to search when you can keep it all within the 'boardscape'.
You can also if you want have both search systems active - default search (from the little dropdown search box) can use BT search while 'advanced search' can still link to the built in vb search.
You can also define usergroups who can still use the vb search (mods/admins for example or perhaps paying members) while everyone else uses the BT search.