Big Black Spot on Main Stem
 

Anyone know what this could be? It worries me a little.

Is it soft at the black spot? Looks like the start of stem rot. You could scrape out the bad spot using a sterile instrument and pack the hole with cinnamon powder. I would do it fast because if it's rot it spreads fast.

It is soft. Damn =( Wonder how it happened!

The potting medium isn't clearly visible but it looks as though it might be old and broken down. If it is old, I would repot the orchid into fresh new large bark, and clean out the rotten spot at the same time.

So I scraped out the hole and covered it with cinnamon powder. Unfortunately I just noticed the hole came back today. Any other suggestions? Should I use Physan 20? I've heard of this before...

I have never used Physan so I can't tell you on that one. You could try putting cinnamon in the hole daily. It may be far into the plant, if it is your plant might not make it.