When playing in a golf tournament if there a penalty for allowing a
group to play through?

Allowing another group to play through is mandated pursuant to the
Etiquette guidelines developed by the USGA.  However, the committee
organizing the tournament can establish "...pace of play guidelines
that all players should follow" and, if a player is found to be in
gross breach of etiquette, can disqualify that player.  Keeping up
with the group in front is strongly encouraged, but does not
inherently result in a penalty if a trailing group is allowed to play
through.

Sincerely,

Wonko

"Pace of Play 

Play at Good Pace and Keep Up

Players should play at a good pace. The Committee may establish pace
of play guidelines that all players should follow.

It is a group's responsibility to keep up with the group in front. If
it loses a clear hole and it is delaying the group behind, it should
invite the group behind to play through, irrespective of the number of
players in that group."

"Committee 

The ?Committee?? is the committee in charge of the competition or, if
the matter does not arise in a competition, the committee in charge of
the course."

"33-7. Disqualification Penalty; Committee Discretion 

A penalty of disqualification may in exceptional individual cases be
waived, modified or imposed if the Committee considers such action
warranted.
Any penalty less than disqualification must not be waived or modified. 

If a Committee considers that a player is guilty of a serious breach
of etiquette, it may impose a penalty of disqualification under this
Rule."

Source: "The Rules of Golf" USGA (2004-2005)
http://www.usga.org/playing/rules/rules_of_golf.html#

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Clarification of Answer by wonko-ga on 04 Feb 2005 15:33 PST

I am sorry my answer did not completely address the specific
information you are seeking.  In the future, may I recommend that you
post all information you have available regarding your question to
facilitate answering it in the most accurate way possible.  In the
absence of knowing there was a particular type of tournament you were
concerned with, I naturally sought the most broadly applicable rule.

Sincerely,

Wonko

I was told that in a low gross competition where individuals play in
flights, it would not be permissable for a 2nd flight group to play
thru and be ahead of a first flight group regardless of the pace of
play.

no, they can play through

Not if the group is made up of substitutions.