I have tried connecting my OPPO 105 to my preamp/processor via both 5.1 analog and HDMI connections for long periods each way. In my opinion the DACs in the OPPO clearly sound better than those in my preamp/processor (a Classe SSP-800). Having said that, my system is highly resolving compared to most and so those differences might not be as noticeable in many less expensive (and therefore probably a less resolving) systems.
I suppose that the main advantage of using HDMI is that the connection in much simpler. Generally a set of 5.1 analog cables would run you a bit more money as well. Then, of course, there is the multiplicity of wires if you go the 5.1 analog route. Also, there is the advantage of being able to use the room correction functions in the preamp. This may narrow the differences in some systems but I still found the analog connections to be clearly superior.
Of course, if you went the HDMI route, it would be much cheaper to get a "3 series" Oppo (e.g a 103 or the forthcoming 203) versus a "5 series (e.g. a 105 or the forthcoming 205).
In my case, there is a hidden advantage to using analog connectors. I often like to listen to music while watching sporting events and as far as I can tell the only way to accomplish this is to use the analog outs whether 5.1 or stereo.
By the way, I did extensive comparisons in stereo as well. If anything, the differences were even more apparent, probably because of the "souped up" dedicated stereo DACs in the OPPO.
I think it comes down to the kind of system one has. Ultimately, the best tool for determining this will be your ears. If you don't think you will be able to hear a significant difference between the analog and HDMI connections, then I would go with the "3 series" OPPO.
Hope this is of some use.
Jim
N.B. There are other reasons for purchasing a "5" series over the "3" series Oppo besides using the excellent DACS in the OPPO. However, the emphasis of this thread seems to be on the connectors so I will confine my comments to that.