I am a web developer in a small web design studio (15-20 employees). It was founded back in 2005 and since that time we've made over 700 different sites (~500 projects, ~300 clients). I started working here in 2011, so I had not participated in any discussions over decisions to use any PM tools. Here's what we have now:
A pile of tables filled with information about domains, hosts, hosting accounts, domain accounts, FTP access, admin panel access, etc. All this information is presented in quite a messy way on a local website.
A small CRM made for internal use; to some extends it is capable of time tracking, global "task" tracking, it stores project-client relations, basic project information and monthly money flows.
Redmine, which is used as a bug tracker for some of the projects.
One shared mailbox.
The problems are:
We still have to maintain websites that we made several years ago (not all of them, hopefully, but still this can not be neglected). Some of them smell. Some require secret knowledge.
Many projects have a huge backlog, it is not stored anyhow except mail history/documents; e. g. you can't tell precisely, whether local and testing versions are synced (without a file manager). You can hardly tell who designed the frontend, who programmed the backend; to learn that, you have to spend some time searching.
An enormous load of important information is stored by mailserver, and messages are not assigned anyhow to projects/clients/issues in internal CRM/Redmine.
The workflow is not yet stable and I guess it never was. Some sites have a precise spec, some do not; I guess, only a couple of them have VCS and 10-20 have passed the testing stage. Most of the testing often was done by clients themself, which is awfully bad.
There is a lot of SEO information associated with almost every site; we have a few interfaces to manage cross-links and seo pages, but it was never something neat.
Now we have faced all these problems, as it gets more stressful to work with old sites. I don't have any big hopes that one system can solve all these problems (almost certainly it will even get worse). But I believe that bird by bird all this mess can be puzzled out and organized.
Strategies, products and workflows are welcome.