This all depends on your server technology and SWFUpload usually can't configure it.
In PHP, if allowed by the server you can call set_time_limit(0); to disable the timeout within the script. However, this may not fix timeout issues that occur while the file is being uploaded (it only applies to the running script which starts after the upload is complete).
Other server technology has timeouts set in different ways. Refer to your documentation.
Server side
This all depends on your server technology and SWFUpload usually can't configure it.
In PHP, if allowed by the server you can call set_time_limit(0); to disable the timeout within the script. However, this may not fix timeout issues that occur while the file is being uploaded (it only applies to the running script which starts after the upload is complete).
Other server technology has timeouts set in different ways. Refer to your documentation.