I just set up ArcGIS server 10.1 and ArcSDE 10.1 on my test machine, my experiences :
1. Finally, I need to configure all my service and sites to match my current existing server which have ArcGIS server 10 and many applications, so I installed Web Adaptor, I had problem, but solved by changing the host file: ( C:\Windows\System32\drivers\etc\hosts , set 127.0.0.1 servername)
I also had problem with webadaptor, but after I completely uninstalled IIS, then reinstalled, it worked.
2. the test machine which had ArcGIS server 10 installed before, so I unstalled ArcGIS server 10 and removed all compononets, since SOC, SOM are not needed any more in 10.1, so I deleted SOM, SOC and ArcGISWebServices accounts.
3. I am trying to figure out too.
4. After installed ArcGIS desktop and ArcGIS server 10.1, without installing ArcSDE 10.1, I created a SDE database using the tool from ArcCatolog, it worked well, no SDE service created by this process. From, ArcCatolog, it seems you can only use direction connection.
I think you can use ArcSDE command to created a ASDE service on, then you can use SDE Commands, your ArcOBject Applications can still use SDE or direct connections.
Later I installed ArcSDE 10.1 on this machine, probably finally ArcSDE commands will go away.
5.But from my testing, you can not simplly publish the ,msd files which you published on 10, you need to use the new tool to publish or created a .sd file.
The things I could not understand is that: when you publish your. sd file , but you still see the process created .msd and .mxd files, for example ( C:\arcgisserver\directories\arcgissystem\arcgisinput\TEST\test1.MapServer\extracted\v101\test.msd, or .mxd)
I don't understand why not like 10, just publish from .msd and .mxd file, for me .
Also, I don't like the webadaptor feature, for me, most machines which we set ArcGIS server on, there will be IIS on, I think it is easier for admin system like before.
It is my experiences so far.