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Preflop: Hero is BB with 5[img]/images/graemlins/spade.gif[/img], 9[img]/images/graemlins/spade.gif[/img].
<font color="#666666">6 folds</font>, Button calls t1600, <font color="#666666">1 fold</font>, Hero checks.

Flop: (t3800) Q[img]/images/graemlins/club.gif[/img], 5[img]/images/graemlins/club.gif[/img], 9[img]/images/graemlins/club.gif[/img] <font color="#0000FF">(2 players)</font>
<font color="#CC3333">Hero bets t4500</font>, <font color="#CC3333">Button raises to t9000</font>, Hero???

Does his min-raise say "made flush", "made top pair with flush draw", or "made bluff"?

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The opponent limped preflop, so this would be my first question. Did he limp to slowplay or did he limp because his hand isn't that strong? In this situation, a raise is almost mandatory by the Button with any playable hand except a head-up monster like AA, KK, QQ, AK, AQ.

My second question would be: Is your opponent shown any capacity to be deceptive, tricky, thinking, intelligent? If no, then his play is likely to be very straightforward.

I think you can rule out the flush. If the button has two clubs, then this flop is a monster head-up. This is usually a no-brainer slowplay, possibly all the way to the river if necessary.

Assuming your opponent is a straight-forward, not too tricky player, this leads me to think of his holdings as:
a) a big pair
b) a big club
c) something else that catches a piece of the flop, maybe QJ, QT, Q9
d) It is possible that the opponent may have a couple of smaller clubs too, like 7c8c or JcTc, and possibly he is raising to protect them.

What are the chances that the opponent hold one of these hands and how would you proceed against the most likely holding?

With this limited information set, I would probably call and see what the turn brings. Most likely I would proceed cautiously. This is a dangerous flop for your holding, relative to what the opponent may hold. You are likely either way ahead or way behind.

What are the payout schedules and where do the other players sit in chip strength? These are other factors for consideration.