I'm sure that I have more than one pet peeve so I'm declaring this to be my first entry on the subject.
This is a sample of a URL that seems ridiculously long:
Is this problem created by FileNet?
I could see repeating onestop if they were trying to get ranked higher for that keyword by search engines, but that can't be their need. It looks like someone created at site and then needed to recreate the site so just put it all under a new directory.
I think there are many who forget that URLs frequently make it into print. And having this long a URL practically guarantees that it will break if sent via e-mail. (Not to mention that's it's hard to read out loud over the phone or to copy down.) I always skip the long URL and create a shorter one with tinyurl.com or similar service if I need to send someone the link. I dont' feel like I should suggest that solution for people creating University documents that refer to the URL.
Bonus pet peeve: underscores in filenames. You put these URLs in print and they get underlined and no one knows if you used spaces or underscores. I think both are poor form.
I have another example: I just had to fix a broken link and the only change was for the directory: jobs to employment. Why make such a change? People use the word jobs more often than employment don't they? Isn't it easier to type? And shorter and therefore less likely to break in an e-mail?