Overly literal search engines reduce usability in that they're unable to handle typos, plurals, hyphens, and other variants of the query terms. Such search engines are particularly difficult for elderly users, but they hurt everybody.
A related problem is when search engines prioritize results purely on the basis of how many query terms they contain, rather than on each document's importance. Much better if your search engine calls out "best bets" at the top of the list -- especially for important queries, such as the names of your products.
Search is the user's lifeline when navigation fails. Even though advanced search can sometimes help, simple search usually works best, and search should be presented as a simple box, since that's what users are looking for.

PDF Files for Online Reading
Users hate coming across a PDF file while browsing, because it breaks their flow. Even simple things like printing or saving documents are difficult because standard browser commands don't work. Layouts are often optimized for a sheet of paper, which rarely matches the size of the user's browser window. Bye-bye smooth scrolling. Hello tiny fonts.
Worst of all, PDF is an undifferentiated blob of content that's hard to navigate.
PDF is great for printing and for distributing manuals and other big documents that need to be printed. Reserve it for this purpose and convert any information that needs to be browsed or read on the screen into real web pages.

Non-Scan able Text

A wall of text is deadly for an interactive experience. Intimidating. Boring. Painful to read.
Write for online, not print. To draw users into the text and support scan ability, use well-documented tricks:
• subheads
• bulleted lists
• highlighted keywords
• short paragraphs
• a simple writing style, and

Violating Design Conventions
Consistency is one of the most powerful usability principles: when things always behave the same, users don't have to worry about what will happen. Instead, they know what will happen based on earlier experience. Every time you release an apple over Sir Isaac Newton, it will drop on his head. That's good.
The more users' expectations prove right, the more they will feel in control of the system and the more they will like it. And the more the system breaks users' expectations, the more they will feel insecure. Oops, maybe if I let go of this apple, it will turn into a tomato and jump a mile into the sky.

Opening New Browser Windows
Opening up new browser windows is like a vacuum cleaner sales person who starts a visit by emptying an ash tray on the customer's carpet. Don't pollute my screen with any more windows, thanks (particularly since current operating systems have miserable window management).
Designers open new browser windows on the theory that it keeps users on their site. But even disregarding the user-hostile message implied in taking over the user's machine, the strategy is self-defeating since it disables the Back button which is the normal way users return to previous sites. Users often don't notice that a new window has opened, especially if they are using a small monitor where the windows are maximized to fill up the screen. So a user who tries to return to the origin will be confused by a grayed out Back button.
Links that don't behave as expected undermine users' understanding of their own system. A link should be a simple hypertext reference that replaces the current page with new content. Users hate unwarranted pop-up windows. When they want the destination to appear in a new page, they can use their browser's "open in new window" command -- assuming, of course, that the link is not a piece of code that interferes with the browser’s standard behavior.

Not Answering Users' Questions
Users are highly goal-driven on the Web. They visit sites because there's something they want to accomplish -- maybe even buy your product. The ultimate failure of a website is to fail to provide the information users are looking for.
Sometimes the answer is simply not there and you lose the sale because users have to assume that your product or service doesn't meet their needs if you don't tell them the specifics. Other times the specifics are buried under a thick layer of marketese and bland slogans. Since users don't have time to read everything, such hidden info might almost as well not be there.
The worst example of not answering users' questions is to avoid listing the price of products and services. No B2C ecommerce site would make this mistake, but it's rife in B2B, where most "enterprise solutions" are presented so that you can't tell whether they are suited for 100 people or 100,000 people. Price is the most specific piece of info customers use to understand the nature of an offering, and not providing it makes people feel lost and reduces their understanding of a product line. We have miles of videotape of users asking "Where's the price?" while tearing their hair out.
Even B2C sites often make the associated mistake of forgetting prices in product lists, such as category pages or search results. Knowing the price is key in both situations; it lets users differentiate among products and click through to the most relevant ones.