Problems migrate database from 4 to 5.5 mysql
This should be as simple as piping the output of mysqldump through a utility that can manipulate the data stream with a regular expression pattern match, like sed or perl.

mysqldump [options] | perl -pe 's/^\)\sTYPE=InnoDB/) ENGINE=InnoDB/' &gt; dumpfile.sql


For any line that begins with ) TYPE=InnoDB this will replace the starting portion of the line with the new string ) ENGINE=InnoDB and leave the rest of the line intact.  It won't do anything to lines that don't match (they'll pass right through).

For quick and simple validation that this does what you want, use the --no-data option in mysqldump to dump only the table structures, not the data, and examine the resulting file.  If it looks right, you can repeat the process without --no-data.

A similar expression in sed should be this:

mysqldump [options] | sed 's/^) TYPE=InnoDB/) ENGINE=InnoDB/' &gt; dumpfile.sql


...however, I'm not as conversant in sed as I am in perl, so I'd recommend the first approach, although I tested both versions and they appear to work identically. 

Both perl and sed should be already present on any *nix system, and both are freely downloadable for Windows.  On Windows, you'll probably need " rather than ' surrounding the expressions.