Development notes: general

Communication is difficult, it's easy to get wrong. Here are some ideas about how to get it right.

Mailing lists: Make them public (within the company). Archive them. Make them discoverable. Let users administer them. See GNU mailman.
Wiki: Only have one. Keep the software up-to-date. Have an 'information architect' role, who manages the structure, so that the information is in predictable places. Make sure the search works (test it regularly). Unlock all the permissions. Let people delete pages. React to user feedback.

When you upgrade, ideally migrate/import the data to the new version. If that doesn't happen, then export or otherwise safely archive the old content. Publish it internally, make sure it's available, even if static.
Use the Gliffy plugin or equivalent (e.g. on ~~Atlassian Confluence~~ an open source wiki) or equivalent to allow users to publish diagrams of unlimited complexity, that can be edited and kept up-to-date by anyone.

Issue tracking system: Keep the software up-to-date. Don't install a million plugins (looking at you Jira) that make it difficult to upgrade. Make sure the workflows match reality, give people standard ones and document how they work. Be very careful when making changes to workflows, try to keep them as general and re-usable as possible.
Write high quality tickets.
Service Desk: Use the same system as the bug tracker, which will allow all staff to track their tickets' progress in a way they understand. If this is not possible, make the service desk ticket system no less usable/visible than the staff issue tracker system.

Ensure the service desk issue system is no less usable than email, i.e. original message chain quoted in all replies, and CCs honoured with reply-all.
Have a special email address for people to CC which will copy the email to a ticket. Publicise it regularly.

instructions for transferring phonecalls internally
instructions for setting up a conference calls (for all phone models in use)
instructions for setting up video calls from conference rooms
instructions for setting up a laptop/desktop with the big screen in meeting rooms/presentations

List all regular non-stream tasks, define roles to triage, co-ordinate and communicate them to the rest of the team, with a view to improving and streamlining the work of the team. Examples:

Ideally don't have any remote members of the team. But at the very least, don't inconvenience the co-located members for the sake of remote members. This means:

Don't hold scrum via phone or skype, hold it in person. Figure out some way for the remote people to attend that doesn't take anything away from the people in the room. If there's no way, they can attend their own scrum, or not at all.

Update: Video chat (e.g. Zoom) works well when there is a large TV screen and dedicated room microphone device. Whoever is in the office goes over to that TV & mic area and starts the video call so anyone working remotely can dial in and participate.

Don't force people to communicate via headsets when they're standing next to each other. That would discard the many benefits of face-to-face communication.
Make sure everyone actually stands up around a physical board (Update: Jira scrum/kanban board works fine over video chat, if updated outside the meeting). If headset range is too far to work, don't use them.
Don't have the scrum at a weird time of day to accommodate other time zones.
If it's difficult to hear the remote members then have them email points to the team.
Try to arrange for the remote members to work one-on-one with each co-located member, to build rapport

Put ALL work in the issue-tracking system to make it visible, even non-development work. If it's not tracked, you didn't really do it. Each task must link back up to team "epics" or long-term goals, and ultimately to a company goal. Must be extremely easy to create tasks with one line of text and no other info, i.e. prevent unnecessary overhead for simple tasks.
Specific to large companies:

Instant chat client for ALL members of staff, with zero configuration, it's just there waiting to be used. Hooked into Outlook and the O/S so that it knows when you're in a meeting or away from your desk and updates your status accordingly (e.g. MS Office Communicator)
Have a meeting room booking system that is painless (is this even possible?) and transparent with regard to: higher-ranked employees permission to "override" bookings, policy for block-booking rooms every week, etc. Above all it should be obvious what is happening and why.

IRC/Slack or equivalent for all. Make it clear that all communications will be logged.
(crazy idea) Employ a person/team whose sole remit is to make it easier to communicate within the company. This is definitely not the usual "Internal Communications" team that sits with HR and serves the Executive. It's a team that is there to support IT workers.
If the office is very large, publish a map of where each team sits. Make sure it's always up-to-date, either by giving a team the responsibility to do it, or making it editable by anyone on the wiki.
Link from the team map to official wiki pages, etc. org chart, make everyone's names and roles discoverable and visually represented.
Put signs up around each area so you can see which team sits where.
Use scrumblr.ca or funretro.io or similar (virtual post-it note boards) for retrospectives, to allow ideas to be captured throughout a sprint, not just on the day. Also a wiki page does just fine. But it's also important to keep real, physical post-it notes and pens in the meeting for people to jot down ideas they just think of at that time.
Create the following types of wiki pages, for each team or development group:

Tech Debt / Yak Shaving / Infrastructure to-do list / Ideas / Suggestions (use your judgement if this should be one page or several). This is a list of things that people want to do, changes they want to make that are not on the roadmap, or don't obviously provide direct value to the business. The team may need help explaining where the value lies.
Proposed technical discussion topics. Topics worthy of group discussion. Schedule a regular meeting (every 2-4 weeks) to discuss whatever is on this list and make a decision as a team about how to proceed.
Developer FAQ. Either per-team or per-department.

Source: My own experience working in IT.

Development notes