I don't know about the allergies being affected (we all have them in the house, and nothing much seems to help), but we've been using window AC units (here in Texas, also) since our central air compressor went out October 2009, I think....
We bought 7 used ones for less than $300 total.... and I think our electricity bill is less, since we are "zonal" cooling. We usually cool the bedrooms only at night, and the LR/Kitchen area during the day. 2 years ago, when we first started this, our highest summer bill was about $350, compared to almost $500 the summer before! For the most part, we only cool the rooms that are being used at that time.
I think we are able to keep the house cooler in general, too. Our old central air compressor was running almost 12 hours straight, and struggling to keep it cool at 82 degrees inside....
Even last summer when we had a record breaking summer (almost 90 days of triple digit temps, I think?) the house was very comfortable. We weren't using all of the rooms, though, since we didn't have a houseful. (2 of the units were in the converted garage - two bedrooms out there weren't being used.)