MySQL has two confusingly identical by the first look variables myisam_sort_buffer_size and sort_buffer_size. Thing is that those two confusingly similar variables has absolutely different meanings.
sort_buffer_size is a per-connection variable and do not belongs to any specific storage engine. It doesn’t matter do you use MyISAM or InnoDB – MySQL will allocate sort_buffer_size for every sort (required most of the times for ORDER BY and GROUP BY queries) so increasing it’s value might help speeding up those queries however I would not recommend to change it from the default value unless you are absolutely sure about all the drawbacks. Value for out-of-the-box MySQL-5.1.41 installation on Ubuntu is 2Mb and it’s recommended to keep it that way.
On the other side myisam_sort_buffer_size used by MyISAM to perform index sorting on relatively rare table-wide modifications like ALTER/REPAIR TABLE. Stock value is 8Mb so if you are using MyISAM tables intensively (please refer to my other post to see how to know your tables type) I would recommend to set it to some higher value close or even more than key_buffer_size but still small enough to keep it in memory and prevent MySQL from swapping.