I can't remember a time when I wasn't cursed with allergies. Fortunately, the majority of my allergies are not life threatening, but they are annoying and can be uncomfortable. And messy. Ah choo! I've learned over the years that not all of my allergies respond to the same antihistamines, so I tend to switch them around, depending on what allergen is currently floating around, and therefore keep an eye on pollen counts.
One of the first pollen count apps I found for my first iPod touch was Zyrtec AllergyCast. Yes, it advertises their own product, but it does give the pollen counts for your area, and a list of the offending flora. It also gives you a weather forecast.
When I started sneezing again a couple of days ago, I did a search to see if there was anything new and better. There is. Allergy Alert from pollen.com. While both apps give the current stats, Allergy Alert also adds a 4 day forecast (the better to plan ahead) and it takes advantage of location services so it can automatically call up the information for your current location, not just a home location that you have set.
Both apps are free, so try them both and see which appeals to you the most.