Being in a northern climate we spend most of our practice time inside. So here is my $.02:
We focus a lot on hitting, as it is the easiest think to do indoors. Use your cage. Get another if possible. Nothing like hitting a real ball.
If you want to go with wiffle balls, then the total control balls are pretty good. www.totalcontrolsports.com. They cost a lot more than regular wiffles, but are much more robust and heavier -- provide better feedback.
You can still throw in a gym, so we do that. And A LOT of conditioning -- especially core work.
Pitchers and catcher's can do most of their normal stuff.
For infield, we work a lot on fielding with the hands. Its all short stuff, but really works the hands. We also work a lot on the double play toss/transfer between the SS and 2b.
We once played dodge ball. Broke up the monotony of being indoors.