A really easy way to do this is to add a UNIQUE index on the 3 columns. When you write the ALTER statement, include the IGNORE keyword. Like so:
ALTER IGNORE TABLE jobs
ADD UNIQUE INDEX idx_name (site_id, title, company);
This will drop all the duplicate rows. As an added benefit, future INSERTs that are duplicates will error out. As always, you may want to take a backup before running something like this…