1. The default use of /usr/libexec/path_helper to manage your $PATH.[1]
2. An accumulation of log files in /var/log/asl.[2]
For (1), I just edit /etc/profile and disable path_helper altogether. I set the PATH manually. (This also allows me to put /usr/local/bin before /usr/bin, which is my preference. I've never understood Apple's default settings for $PATH. They put /usr/local/bin later - which defeats the whole point of installing, say, a newer vim in there.) For (2), a cron or launchd job can take care of it.
[1]: http://mjtsai.com/blog/2009/04/01/slow-opening-terminal-wind...
[2]: http://osxdaily.com/2010/05/06/speed-up-a-slow-terminal-by-c...