How can I log slow queries in mysql?

Add these lines to your my.cnf (usually in /etc/my.cnf)

log-slow-queries = slow.log
long_query_time = 20

This logs any queries that take longer than 20 seconds to a file called "slow.log" in your data directory.  Your data directory should be in /var/db/mysql, or /var/lib/mysql on a unix system.

NOTE:  You need to restart mysql to have these changes take effect - usually run this command: 

/etc/init.d/mysql restart 

Anyway the logs generated here should help you pinpoint any queries that are really bogging down. 

AFAIK, this setting doesn't slow down the server much, unless a lot of queries are getting logged.  But if you are not actively checking for slow queries, you should probably turn this off.