XenServer is a bit of an odd one to me. We sometimes use it for Server Virtualisation, but we now primarily roll it out for Desktop Virtualisation (VDI) in which it does a very good job.
If it was a choice between current Gen Hyper-V and XenServer then I'd personally go for XenServer, but that's because I know it better than Hyper-V. I certainly don't think it's any worse than Hyper-V, but I'm not convinced it's objectively much better, either.
To say it has a few oddities would be an understatement, and the GUI is fairly limited meaning you very rapidly end up in the console whenever you want to do anything remotely exotic.
It's potentially less stable than Hyper-V, especially once you get into multi server (They call them "pools") deployments, but at the same time, it's also very rapid to deploy and fix so it's swings and roundabouts really. Also, this is purely anecdotal and we have may more XenServer customers than we do Hyper-V.
To be honest, the current generations (I'm excluding Hyper-V 2012 here) aren't a patch on VMWare VSphere and so if cost is lower down the priority list than most other things you almost certainly want VSphere. Other than that, take your pick based on cost/features/local expertise and accept the niggles!
That all said, I think VMWare need to watch their backs because everything else is getting better and VSphere is shockingly expensive still! I'm really looking forward to getting hands on with Server 2012 when I get off my summer projects.