I've got a fairly simple SharePoint 2010 farm set up: 2 WFE servers with Network Load Balancing hosting the main portal site.
As per Microsoft's best practice recommendations I've set up My Sites in a separate web application. As some of the user base are not using domain joined PCs they have to login once for the portal (http://portal) and then again when the access My Sites since they're crossing in to a separate web application on a separate host (http://mysite). Portal & MySite are both hosted on the same physical WFE servers.
Is there an easy way to set up some thing to stop this happening and just have them login once?
I understand that there's plans for us to deploy ISA in the not too distant future - could we use ISA to manage authentication to the two sites so that the users only need to log in once?
An easy way built into SharePoint? No. Your choice is really to move the MySite collection into the existing farm, or deal with the authentication issues.
ISA is going to be the easiest way to deal with this. It can capture the user credentials and reuse them on all (or select) backend connections. It is what we use right now for single sign-on to a farm of various servers and applications.