MySQL - Changing DB CHARACTER SET
I know what you mean. Alter table sometimes has to rebuild the whole table when you use it. 

Assuming that the Alter table statement is annoying you because it takes too long AND it locks your table, then you can use 2 tools to make it an "online" alter table.

One if from facebook https://www.facebook.com/notes/mysql-at-facebook/online-schema-change-for-mysql/430801045932

And one is from openark http://openarkkit.googlecode.com/svn/trunk/openarkkit/doc/html/oak-online-alter-table.html (MySQL 5.1+ only)

Both these tools basically create a new table, copy the data over and keep it updated by updating both the old and the new table with new queries until the new table is completed.
This means that you need to have the space available to do this operation.

Hope it helps.