According to the MySQL manuals, you only have a limited number of options:
Use lower_case_table_names=1 on all systems. The main disadvantage
with this is that when you use SHOW
TABLES or SHOW DATABASES, you do not
see the names in their original
lettercase.
Use lower_case_table_names=0 on Unix and lower_case_table_names=2 on
Windows. This preserves the lettercase
of database and table names. The
disadvantage of this is that you must
ensure that your statements always
refer to your database and table names
with the correct lettercase on
Windows. If you transfer your
statements to Unix, where lettercase
is significant, they do not work if
the lettercase is incorrect.
Exception: If you are using InnoDB tables and you are trying to
avoid these data transfer problems,
you should set lower_case_table_names
to 1 on all platforms to force names
to be converted to lowercase.
See: http://dev.mysql.com/doc/refman/5.0/en/identifier-case-sensitivity.html for full details.