Performing a large migration exercises a Drupal installation in different ways than normal production usage. There are several things you can do to improve the performance of your migration processes.
If you are going to upload large files through Table Wizard, you should increase the following parameters, as well as increasing Drupal's maximum file upload values:
php_value max_input_time 600 php_value upload_max_filesize 255M php_value post_max_size 255M
Bulk creation and deleting of nodes and users can strain memory usage - you should consider significantly boosting memory_limit:
php_value memory_limit 256M
When performing a migration process, whether interactively, via cron, or via drush, the Migrate module monitors execution time and exits a few seconds before max_execution_time is exhausted, to avoid partial updates. To get the most out of each processing step (in light of cron's limitation to 240 seconds max), set max_execution_time to 240 seconds:
php_value max_execution_time 240
In normal Drupal usage, nodes and users are created and deleted one at a time - thus, the core is optimized for that kind of load and is not well optimized for the bulk operations that the Migrate module performs. The following patches are recommended to help your performance when performing migrations.
node_delete() unnecessarily caches the node being deleted - when hundreds or thousands of nodes are deleted in a single request, you can very quickly run out of memory. Go to issue #287063 and apply the patch in comment #8 to prevent this caching.
Deleting a user updates the comments and node_comment_statistics tables rows referencing that user's uid, but those columns are node indexed, making deletion of users in bulk very slow. The patch at http://drupal.org/node/289504 addresses this.
Note: These patches have already been incorporated into Drupal 7.
When using the Email registration module, if you would like an explicit username you're migrating to override that module's automated username generation, apply the patch at http://drupal.org/node/247717.