Silicone sealent on a bong?

Yes, I use it all the time on my homemade bongs. To this day I haven't found a better substance that does the job.

And as for brass pipes, I've been smoking out of those for years, and never heard they are bad. Copper is bad and I always stay away from that. However I used to smoke out of beer cans all the time. No problems with me that I'm aware of.

You could buy orange RTV from an automotive store. RTV orange is high temperature sealant, and i think it's good for over 800-1000 degrees. I use it for exhaust gaskets when i'm in a bind.