Best way to bypass Squid for certain sites?

If you want to AVOID completely squid, adding exceptions to the transparent proxy iptables redirect rule is way.

You can, however, create an acl in squid for the always_direct directive. From the squid docs:

acl local-servers dstdomain my.domain.net
always_direct allow local-servers

It doesn't work in all cases, sometimes just avoiding the proxy completely will do.

EDIT: If you use something like shorewall you can create lists that make the exception for the redirect rule easier to manage, but it may be too overkill.

I don't think always_direct configuration directive would be the appropriate choice - it simply specifies to not contact parent or peer caches, does not affect whether the web site itself will be cached.

Take a look at the Squid FAQ: How do I configure Squid not to cache a specific server?, regarding the cache directive and ACLs