My brother has the old Saginaw out of my Malibu in his 69 Caprice.

He does not hammer this car at all and he has driven it very gently as the 427 in front of it could reduce it to rubble very quickly.

He went to back it up today and heard a loud bang, after that the trans makes a clicking noise above 25 mph. It still has all it's gears working and shifts fine. Needless to say it is parked just as cruise season is beginning :(

Unfortunately money is very tight for him, I know most will say to get a Muncie, but he just cannot afford it at this time.

Any thoughts on what could have broke?

Just pull it out and open the side cover to see just what's wrong as there's not much point in guessing.

What Mike said. Pulling it doesn't take long at all. Put the front end up on ramps, rear end on jack stands, un bolt the drive shaft, slide shaft out, unbolt trans from bell housing and then slide it out. The trans will have to be in gear when you unbolt the caps that hold the drive shaft in place. Be sure whatever shifter handle you've got is taken off of the stick. Also, be sure to stick a yoke ,or seal, in the rear of the trans after you pull the drive shaft.

I've been running these saginaws since I was a kid, and have a few parts lying around.
The trans is probably the easiest one out there to tear down and reassemble. A good hammer, brass drift, snap-ring pliers and some wrenches is about all you need unless you have to press the synchronizers off the main shaft.
Once he finds out what's broke, PM me to see if I have anything he can use...little something to cover shipping is all I would need.

Jeff and everyone, I appreciate the advice and yes we will be removing it to see whats up with it!!

Jeff, I appreciate the offer and I will let you know if we need something.