Keano
I'll try to answer both of your questions, although neither has a direct and easy answer.
1. USB is dependant on the protocol you are using to connect primarily. With pure RDP you won't get much in the way of USB. Other protocols and add-ons to RDP (dependant on Thin Client), etc will all have their own feature sets with what works and doesn't work with RDP. There are options like "AnywhereUSB" from Digi (http://www.digi.com) or "USB over Network" from FubulaTech (http://www.fabulatech.com) which can help as well. For starters, what make/model of Thin Client are you working with?
2. The "best" tool is hard to define and up for debate I'm sure. You can convert machines with VMWare's converter (what used to be P2V) from a real physical machine. Other companies offer their own P2V converters as well, but I've found VMWare to be far more than sufficient personally. You can also build your Virtual Desktop directly on the VM machine. That all depends on your standard imaging process you are currently using, but almost all technologies will work directly to a VM. You could build witih BDD, ghost an image over, or even perform a manual installation.
Hopefully that helps a little...
Thanks
Steve