I've been given the job of creating our corporate website. My
colleague, who has been working on this project for several months,
has chosen to use a pre-existing CMS rather than build a site from
scratch. He has convinced management that this would be the better
option, but personally, I would much rather build a custom site given
the specs decided on by the management. His argument against building
a custom site is that it would end up being built in such a way that
another developer, should something ever happen to me, would be unable
to decipher my code. He argued that I would not be able to write
enough documentation to avoid such a problem. I've been building
websites for over 10 years now and I have been asked on many occasions
to decipher and modify code written by other developers. I will agree
that it can be time consuming if the developer hasn't take the time to
properly comment their code, but I've never come across anything I
couldn't handle. I argued that this would also be a problem pre-built
CMS as it will take time for me to decipher the coding style of many
developers. I also argued that given the number of different
open-source CMS' out there, finding a developer who would be familiar
with this particular CMS is unlikely.

We are a multi-department organization and each department would like
to have its own website. Currently, we are setting up a separate copy
of this CMS (each with a separate database) for each department. Each
site is independent from each other, but they would like to be able to
share data between sites. The chosen solution is to modify each site's
search engine to also search the others. We currently have 6
departments set up but will have as many as 10 in the near future. I
can already see this being a huge headache to administer, but also, as
our organization grows, keeping up with changes made in 10 independent
sets of code will become even more of a headache!

My opinion... why have 10 separate sites which need to share data when
you can build one? I feel that the chosen implementation, while it
gives us software which has been written by many developers with all
their ideas and updates (which will prove useless due to the extensive
customization required) will prove a complete waste of time. But then
what do I know. I'm just a lowly web developer with more than 10 years
experience who was hired to build this website because my colleague,
who has made all of the decisions so far, lacked the knowledge and
experience to build the site in the first place!

Anyone have any advice? Or even just an opinion?

Moved to Web Design and Content .

It makes absolutely no sense whatsoever to manage separate databases for each Web site. I think you/your cohort may have assessed the company's needs in the reverse order. You start by identifying everything you need, regardless of the technology that exists, and then you look to see whether the technology is out there that can handle what you need, or whether you need to start from scratch, or do a hybid of the two. If a thorough needs assessment has been done, the answer to whether you use a CMS-in-a-box versus custom CMS will answer itself.

But yes, maintaining separate databases for a single greater entity is stupifying.

I agree...One site is more than enough to handle. You're company will be very sorry going down the 10 separate sites road.
Although fine for personal sites, I'm sure that your company will want to do things that the CMS won't be able to handle.