Things that raise *my* blood pressure when booking flights:
(0) The total absence of any kind of universal transport management system. Want to make a connection from a flight to a train? SUCKS TO BE YOU.
(1) The terrible, terrible user interface. Fill in outward journey, press search. Oh, look, I haven't filled in the return journey, so instead of assuming I want a one way journey it just fails with an error. Select the 'one way' checkbox. Outward journey details get cleared. Fill in outward journey again... sigh. Plus, of course, you have to use a selection of badly-designed custom widgets and drop down boxes to do all this, and no two airlines' work the same, and frequently they don't work at all. Tip to UI designers: drop-down boxes for day of month is *stupid*.
(Still, the airlines do this better than the railway companies. The only way to find out whether a given London-Inverness sleeper train has vacancies is to actually try to make a booking.)
Oh, and the session timeout is usually way too small, so if you try to compare two flights in different tabs, the details all vanish when you're not looking. I think Easyjet's is something ludicrous like five minutes.
Deselecting all the extras I actually don't mind too badly --- it's just something I've got used to. Doesn't mean I like it, of course.
(2) The stupidity that is Mastercard Secure / Verified by Visa.