Here's the difference between the two, as stated by Google here.
The main difference between the
Search-based Keyword Tool and the
Keyword Tool currently in AdWords is
that the former generates keyword
ideas based on your website, and
identifies those currently not being
used in your AdWords account.
Additionally, the Search-based Keyword
Tool provides more detailed data for
each keyword, such as category
information, suggested bid that may
place the ad in the top three spots of
a search results page, and ad/search
share. Both tools, however, offer the
option of browsing all keywords across
all categories.
You may also notice that some of the
data (like such as the monthly search
volume) may vary slightly between the
two tools, which is due to different
methods of calculation at this time.