Hi All,
I assume when you said Microsoft PWA that your company is using EPM. From my expereicne (I'm the Lead EPM Consultant at my company) I'm sure that you can use EPM timesheet and resource mangement to your likeing. its just matter of what and how to use it.
One solution can be to have a resource manager. The resource manager would be responsible to aasigning resources to projects and hence, he would be responsible for their avialability.
Another solution would be (if your are using EPM) is to use Administrative template along with the project itself to track the resources vacations, seeing a doctor, training, etc.. (off project time). This way when you check the resource availability you will have all the variables.
What John mentioned in his comment is actually what MS EPM does. After creating the project plan and saving a baseline for it, you can always have baseline (planned) and actual task duration for each resource. add administrative tasks to it and you will get the full resource time on daily bases :)
I'm sorry if I sound like I'm marketing a product but its something I'm pretty good at and know of ;)