Pick the one that suits you best.
If your webservices are invoking EJBs I would suggest you use JBoss.NET because (a) JBoss handles the integration between Axis and the container and (b) deployment will be easier.
The issue of portability is mute in my mind. WSRs are more in keeping with the standards, and in a porting scenario, re-packaging your deliverables will not be a large amount of work; issues like configuring CMP will cause you more headaches.
Lastly, I am following the .NET route, and the more people that do this, the easier my life will get :)))