Mike,
We've been real windy up north in Sacramento and we're in prime allergy season. The other day I lost my voice for over an hour while making errands in downtown. I did the allergy shots for 10+ years and now I just "deal with it" as most of the allergy medicine makes me groggy or creates other problems (nose bleeds, dry mouth, etc).
While I can offer no medicinal recommendations I've had pretty good luck with my neti pot every morning and find that after a week of riding with the pollen that my body adjusts.
One of the guys I ride with on my morning commute (when I can catch him) recommended: Xlear Netixlear Saline Nasal Wash with Xylitol. He found it to be much more effective in 24-hour effectiveness. Apparently the Xylitol salt (or whatever it is) does a good job in leaving a protective coat on the nasal passages.
I haven't yet consulted with my physician but it's got glowing reviews on the 'net from what I consider to be reasonably acceptable sources.