Sorry about being a little late to the party, but I thought this sounded a little interesting, as the thread allows the oppotunity for insightful comments.
1) Underestimating the A320. This cannot be stressed enough. Boeing's failure to accurately estimate the impact Airbus would have with the A320 is the greatest failure in recent memory. It wasn't until the much publicized defection of UA from the 737 Classics to the A320 that Boeing finally woke up.
2) The delay in launching the 737NG Program. As mentioned above, Boeing really missed the boat with the United order. They could have had the opportunity to make a similar arrangement with their largest customer as with the 777 Program. Instead, they decided to push the inferior 737-400, and suffered the inevitable consequences. It wasn't until Southwest asked for a better 737 that Boeing finally got its act together, and produced a competitive (and in at least one case, superior) narrow-body. This can be attributed to. . .
3) Boeing's arrogant attitude in the '80's to mid-'90's. As well explained by Philly phlyer above, Boeing's approach to their customers, particularily their U.S.-based ones, was downright attrocious. When one believes one's place is assured is when you find out it is not!
4) Certain derivatives of programs. In the long run, I would call both the 747SP (should have developed a longer-range 747-200 instead) as well as the 747-300 (should have concentrated on the -400, and brought it out sooner) if not mistakes, than at least short-sightedness. Along this same line, you could call both the original 727 (i.e. -100) and 737 (i.e. -100) as ignorant to what the market was truly asking for and needing - more capacity.
What are NOT mistakes
1) The 767-400ER and 757-300. Both these aircraft were derivatives of previous, successful programs. Especially with the 753, these are 'minimum change' derivatives that are designed to appeal to a more select customer base. In addition, one must take into account that the future of these programs are still very much undecided, and any classification is premature, at best.
2) The Sonic Cruiser. How anyone can classify a program that has yet to be launched a failure is quite frankly beyond me. Especially one that has the potential to be ranked as one of the most revolutionary commercial jetliners in history, among the select group of the Comet, the 707 and the Concorde.
Just my thoughts.