Looking for some feedback before going down this rabbit hole...

I can turn off hyperthreading but I like the flexibility it provides. I can leave tasks running while I work or game and there is no noticeable degradation in performance. BOINC tasks will run a bit slower when there's more going on, but I'm ok with that.

I found some powershell examples for getting and setting affinity but I have not tested them out. My thought was to create a scheduled task to look for unconstrained tasks and reassign CPU affinity.

http://stackoverflow.com/questions/19187241/change-affinity-of-process-with-windows-script

Another option is wrapping the command line with a script that automatically generates the 'proper' affinity mask when launching a new task. Basically, generate the mask, write out to a text file for next run, launch boinc task. Next time through, read previous mask, increment as appropriate, etc. I'm not sure if we have access to the command line for each project or not though.

No definitive results just yet but my estimated remaining time skips a second every ~3 seconds. Far from scientific but I just made this change manually on a few tasks so it'll take some time to see how much of an impact it truly has.

Would this be defeating any process/thread management done by BOINC or Milkyway itself?

I use a program called Process Lasso to fix affinity when I need to.