I'm not 100% sure this isn't a bug in mysql, but here it goes:

I installed mysql 2.23.39, apache and php4.0.6 a few days ago, and
I've had to restart mysql every morning because mysql_pconnect()
fails as the connections have timed out (wait_timeout is set to 8 hours).

First this is logged by mysql (a few times):
010726  6:28:43  Aborted connection 299 to db: 'lumad' user: 'lumad' host: `localhost' (Got timeout reading communication packets)

Then when I try to pconnect PHP logs this:
[Thu Jul 26 11:23:36 2001] [error] PHP Warning:  MySQL:  Link to server lost, unable to reconnect in /export/home/carl/apache/htdocs/db.inc.php on line 8

And after a few more retries I get this:
[Thu Jul 26 11:31:46 2001] [error] PHP Warning:  Can't connect to local MySQL server through socket '/tmp/mysql.sock' (111) in /export/home/carl/apache/htdocs/db.inc.php on line 8

At this point /tmp/mysql.sock has disappeared, and to get it to reappear
I have to restart mysql.
I've considered raising wait_timeout to infinity, but then there'd be problems
if a (non-php) program forgets to call mysql_close(). For now I'll just
switch to mysql_connect().