I replaced the original 500GB HD with an SSD (120GB OWC Mercury Electra 6G). When I found the iFixit Mac Mini Dual Hard Drive Kit, I decided to put the original HD back in the box for additional internal storage. (I use the SSD for the boot + system disk.)
With the iFixit guide, it went very smoothly-- I knew exactly what to expect. With the Kit, I also had all the necessary tools to do the job. It took less than half an hour to complete, maybe could have gone a little faster if I wasn't being more cautious than usual-- the Mini is still under warranty!
I have the Mini at the bottom of a stack (below an external HD and DVD-R). The case of the Mini is very warm to the touch, but it was already pretty warm with just the SSD inside. I've heard the fan kick in full-blast a few times. I've added a spacer between the Mini and the external HD above it, to allow more airflow. I'll monitor this the next few days. If it seems too hot, I might end up pulling out the HD.