I have a PS3 and a Xbox 360 with HD-DVD add-on, and I couldn't imagine trading that for a standalone combo player. However, I'm also a gamer so the choice is easy for me.
However, if I was purely a HT enthusiast with no interest in gaming, I would probably get the standalone. For one, the remote control for the combo would be superior. The HD-DVD add-on came with a decent remote, but I just programmed all the functions into my universal remote. The PS3, however, requires the use of Bluetooth, so I'm stuck with using the PS3 controller. It's not a pretty thing. Yes, you can buy the PS3 remote as an accessory, but to me, that is a disadvantage.
For the Xbox 360 HD-DVD, the lack of support for lossless audio, even with the Elite model, is a huge negative for high-end HT enthusiasts that want the very best. For this reason alone, I think many videophiles would be turned off by this solution.
The PS3 seems to be a fine Blu-ray player, and even has SACD built-in, so certainly it's no slouch. It also seems to support any of the audio options available on BD, so there's no compromises here.
Other than that, I think it's mostly an aesthetic choice, and also a choice of convenience. Obviously with the combo player, your video and audio connections get reduced by half. Actually it's quite nice that with the combo player, all you really need is one HDMI connection. So the choice is pretty simple, I think. If you're into gaming, then the consoles are the easy pick. If you want nothing to do with gaming, then a combo is your choice. If you however have an interest in gaming, but also desire the best possible audio choices for your HD, then that's a little bit harder. Possibly you may consider a PS3 for the BD player, and a standalone HD-DVD with the lossless audio options.