Yosemite upgrade process stuck for hours - Cmd-L not working
Alright so I waited it out only to come back this morning to see that it was still stuck. I've waited several more hours until 10 am this morning which comes down to a total wait of 18 hours. I went ahead and manually rebooted and it looks like the upgrade was completed successfully after all.

Please note that this is not me suggesting you should reboot if the installation seems stuck. In general you should just be patient and wait. In the first phase of the installation press Command-L to show the installation log and you can verify it's actually doing something. Note that it can take a while for the installation log to show up after pressing Command-L.
In the second phase if it gets stuck you can't view what it's doing so it's pretty much a gamble if you decide to reboot it when it seems to be stuck.

I rebooted with my external backup hard drive disconnected to make sure my backup stays intact when things turn sour after all.

I verfied the disk and the permissions with Disk Utility and some permissions were off so I've repaired those. I'm now in the process of fixing Apache, but I'm guessing that's because of the differences between Apache 2.2 and 2.4.