So his phone already had apps and games and what-not on it, I assume purchased with a different account, yes?
And then you created him a new OS X account, logged in under that, then synced the phone to a virtually empty iTunes library, right?
How did you set up the phone initially when you first plugged it in and opened iTunes under his account? What one would expect to happen in this situation normally is that the phone would be wiped clean and synced with the iTunes library it's connected to... I suspect this is what happened and why you say his apps were gone.
One thing to understand about the iPhone and/or iPod touch is that they sync with one and only one account, which also implies that they sync with one and only one computer. If you currently sync with one computer, then take your iPhone to a different computer and sync, the iPod will be wiped out and whatever is on the new computer will be copied to it.
Also, you can think of it as a one-way sync in most cases -- data goes from the computer to the iPod/iPhone, and never in the reverse direction. This is why you can't download a bunch of music to an iPhone using one computer, then take it to another computer and copy the music from the iPhone to the new computer.
Of course, there are some cases where data does go from the iPhone to the computer, but all of that should be transparent to you -- the idea here is to keep an iPhone synced with one and only one computer, under one and only one account. Any deviation from this will most likely result in a wiped iPhone.
Since you're starting him off with a new account under OS X, it may be prudent to get every device on the same page and start off with a wiped iPhone and re-sync everything that needs syncing (remember: computer to iPhone only, so if there are contacts on the iPhone that you want to keep, back them up [with paper and pencil or something] because they will be replaced with contacts on the computer).
Try connecting the iPhone to the computer, ensuring all cables are connected and secured to the iPhone and on the back of the computer or USB hub, then restart the computer. Log in under the boyfriend's account. Open iTunes. Does the iPhone now show in the sidebar?