-I have to say one of the most irritating things for me is searching for mile earning and burning promotions. Sometimes it's under Special Offers, but sometimes that only means discount offers, not mile promos; sometimes it's under How To Earn Miles, or Earning Miles, or Promotions, or Deals, and sometimes its only in the Newsletters, which can take forever to load. There is a difference between explaining how the program lets you earn miles, and the bonus mile offers. Make it obvious where the FF prog mile promos are.
-I don't like it when all the offers are all mixed in together- 20% off fare deals mixed in with the miles earning promos. I want to be able to find ALL the current promotions for earning miles and see them at once, and then be able to see all the cheap fare or hotel offers at once on another page. Some people are going to be looking for the cheapest fare, while some are concerned only with the bonus miles they can earn, or the best award redemption deals.
Some good sites that do this are CO (one of the best, IMO), Cathay Asia Miles, and Midwest. Also- Aeromexico has this type of page setup, however, they only have it for their Spanish site, not English too. So if I want to understand all the details, I have to copy and paste each promo into a translation site, which often ends up lacking in the translation anyway.
- Show me a list of ALL partners at one time. I don't want to have to search in 16 different links to find who all the partners are.
-Another pet peeve? When I can't find all the details and rules for the promotion... some programs leave off expiration dates, or don't tell you exactly what link to find the terms at, etc. Give me all the info about the promo at once, a la NW or United.
- Also, one of the coolest and most unique pages is one I came across on SPG:
http://www.starwoodhotels.com/prefer...tive_grid.html
Makes it nice and easy to compare all the details between programs at once. Use FACTS for things like this, not exaggerated claims, however!! Trust me, FT'ers will see right through "creative wording" and omissions.

-ditto on the crappy calendar pop-ups. half the time they take 5 minutes to load anyway, so i've typed in the date manually already.
-ditto on the advanced flight/fare searches. If i find that searches on your site will give me more info and CHOICES about the ticket, fare, class, etc. and i find fares that will be cheaper and not hide the fees/taxes until after purchase, I'll come back over and over again.
-ditto on the dream map/searches... where can i go for $150 or 15,000 miles....EXCELLENT idea!! Often i'll take a trip I hadn't planned on. But make sure that this will show ALL possibilities, not just 2 or 3 "featured destinations".

Hope this helps!