My personal favorite experience was being called (on my desk phone) by a recruiter in response to an application that I submitted, for a different job at the same company. I had applied 4-5 months previously, and had been working there for at least 3 months. One hand seriously has no idea what the other hand is up to.
I sympathize with you, this can feel pretty bad as an applicant (especially if you've done a lot of work on your resume / cover letter just for that job). Once I realized how things work on the back end, I stopped caring or even thinking about jobs until an actual human reached out to me.
(Or the US does thing entirely differently - I only work in the UK business unit, so you never know)
I'm sure no one actually got/read my CV. It irritates me to no end that I can't talk to an actual hiring manager, can't provide a cover letter, etc.
I recently went through a job hunt and two stand out in my mind: Red Hat and Rackspace.
Neither one of them insulted me or anything, per se. Rather, I saw that they were looking for engineering people on a couple different job boards and instructed you to apply through their 3rd party system. I had done a lot of work lately in virtualization and distributed computing and these guys are good open source citizens there, so I figured I'd apply. Two months have gone by now and still no word -- my status on their website remains "resume received".
Makes me wonder how they ever manage to hire anyone at all. It's really soured me both to them and companies that use that shitty application system in general. At this point I figure anyone who uses it (including Amazon and Oracle) aren't even worth wasting my time messing around with.