I have used a number of applications for collaboration within my firm eSolia and with clients over the last number of years, and I thought I would share the experiences I have had with you.
Groove - we used this before and after it was acquired by Microsoft, and it was promising. We stopped using it because of the lack of searchability and the fact that it was a memory hog. A real catch-22: the more you get into it, the slower it got and the more the lack of search became problematic. Further, when everything went into Groove, if a person left the team, they might also take a part of a project with them, if you were not careful. We got around this by always joining a phantom member to the projects, and the member was just logged into a PC on our network. It had everything in it.
Mantis - we tried to modify this famous bug-tracker for use as a ticketing system for IT support, but this was a stretch without a full time programmer / sysadmin to maintain it. We used it for a while and it just did not cut it, for us. Granted, we were using it outside its scope.
Sharepoint - like many things Microsoft, this file-centric document sharing application can do a lot, especially if you license various plugins to use on top of it like a Project server. However, even with various "add ins", it still had to be programmed to make it do some pretty basic things. Long term we were not impressed, and felt open-source solutions were much better "out of the box".
Trackstudio - this troubleticketing and bug tracking program is a very interesting and cost-effective program, but there were security problems with a couple upgrades a few years ago. Just to ensure client information security, we had to abandon forthright after the problems upgrading, but I want to emphasize that our decision was not based on Trackstudio's people or support, because the support was exemplary; shockingly good.
Atlassian Confluence and Jira - this combo of a wiki and ticketing system is superior, but there were too many things that were "just not quite enterprise." Further, Atlassian had an odd approach to fixing problems, in that they wanted people to "vote" for what they want, and only if the feature got enough votes would it get implemented. Hence, some really important features in the area of security and ease-of-administration were simply left off. My staff liked Confluence but disliked Jira, in terms of usability for our IT Support business in Tokyo, but ultimately we abandoned it.
What's in our Current Stable of Apps
We currently use a number of great applications.
Salesforce.com "email2case" - since we use SFDC for CRM anyway, when we heard about email2case, we did a pilot of it, and found it easy to set up and use. Email2case is a Java jar app that you run on a server, and it polls an IMAP mailbox per customer, putting any mail that comes into the box into a case for the company in SFDC, and assigning a ticket number. Sales staff can see tickets as "Cases" under the customer account. Very easy to keep up with what's going on, support wise.
Mindtouch "Deki Wiki" - this is the best wiki, as far as we are concerned. Very easy to set up either directly on your server or as a virtual server, has S3 support for attachments, is mashable with a huge number of widgets or gadgets, and has great wysiwyg editing that makes adoption easy.
Google Docs - For some situations, it is great to be able to collaborate on docs while you are creating them, real time. Need to keep abreast of what Google is doing anyway, in case it takes over the world (only half joking).
Replicon WebTimesheet or Harvest - these are time and expense tracking applications. WebTimesheet is a little more seasoned, but I expect Harvest will catch up. We can enter Japanese in WTS, but not in Harvest. Implementing WTS allowed us to save weeks of person-time every month collating time and expense spreadsheets.
Others - sometimes, 37Signals Basecamp, or task list apps like "Remember the Milk" and Toodledo.
I hope this list helps someone get started with collaboration. Enjoy!