We recently moved into a new townhome and got an air filter on our furnace like the one Alcie has described. Like her, we keep our fan running all the time. It helps distribute heat/cool and moves the air through the filter constantly.
That said, there are some higher quality air filters (more expensive) that you can buy for your regular furnace air filter requirement. It can't hurt, and will probably help you.
I told my allergy/asthma doc that I had a furnace filter, and he still wanted me to use an air purifier in my room in addition to the furnace filter. I like white noise, so it works for me. I've actually used one for years, but only have had the "deluxe" furnace filter for 3 years. Mine sits on a table top. Just go online and search for air purifiers, and you'll find a wide range of them. My allergist likes the ones that use an actual filter and isn't a fan of the electromagnetic ones with the blades to rinse.
Have you discussed the mold problem with your allergist? I remember quite some time ago (a different city and different allergist) that I was given a script for a mold inhibitor/remover that you mix with water and spray on the offending area. Give your doctor's office a call and see what they recommend for your windows.
Nissen Fundoplication 2/09
"Whatever you fight, you strengthen, and what you resist, persists.”
“Worry pretends to be necessary but serves no useful purpose”
“Accept - then act. Whatever the present moment contains, accept it as if you had chosen it. Always work with it, not against it.”