The place to look for what happened in the failed boot is in /var/log/syslog, and possibly other files in /var/log. However this only works if the logging service (syslogd) had a chance to start. In your other question, you mention an hwclock-related freeze, and hwclock is first executed before syslogd, so maybe no logs were written.
The boot and shutdown scripts are in /etc/init.d. Which ones are executed and when depends on symbolic links in /etc/rc?.d. First the system boot scripts linked from /etc/rcS.d are executed, then the ones in /etc/rc2.d, and the number after the S in the name of the symbolic link determines the order in which the scripts are executed. If your system uses Upstart, scripts in /etc/init are also executed, in an order determined from dependency declarations.
If your system freezes when setting the clock, chances are that you need to add --directisa or some other obscure option on the hwclock command line somewhere in /etc/init*/hwclock*.