Basecamp is an online tool for simple project management. We've used Basecamp for over 3 years to manage projects at SpinWeb. Here are some tips we've picked up along the way:

1. Basecamp is for the Team. For over 2 years, we followed an "Everything in Basecamp" mantra. All emails to clients came from Basecamp. Clients could see todos & milestones. We found is that Basecamp is great for tracking tasks, delegating, and communicating with your team. We found out that clients didn't really care to see the details. They were asking for the big picture; not the behind the scenes tour.
2. Email is for clients. Out of 80+ clients who had a project managed in Basecamp, only 3 of them played by the rules we set up. The rest would forget passwords, email us directly, or just get frustrated. Basecamp emails creeped them out. Training them on how to understand Basecamp didn't help. They just wanted a website, not learning how to communicate by our rules. 
3. Be Inbox Zero. Now we keep our communication with clients in simple emails. Using Inbox Zero for email management, it's easy to find the last reply, CC anyone who needs to know and get things communicated. I don't even have client folders (GASP!). Learn client's names; then use the search tools in your email to find the last email to / from them. It's super easy.
4. Maximize Project Templates. This is a newer feature and is the best time-saver I've found. We have a system that all of projects follow, but now I can create to-do lists, milestones, and link them together before a project is even created. You can also default which members of your company are on a project template. It's awesome-sauce.
5. Use Active, On Hold, Archive. This helpful setting gets me into trouble. When used well, it keeps the Active projects at the top of the list. On Hold projects are grayed out and down at the bottom of your dashboard. The problem is that On Hold projects don't show up on the dashboard, so they can be easy to miss if you assign tasks/milestones and forget to make the project Active again. Archive is great, it puts the projects on a totally different page and hides them away so you don't cry when you see that project that didn't go so well years ago. 
6. Subscribe to Project Updates via Email. The lack of project updates from Basecamp is the area that's almost a deal-breaker for me. As project manager, I like to know when things get checked off - or when they haven't been worked on. This feature sends me an email each morning when something happens in the previous 24 hours. It shows me any new or checked off items. Mostly, it gives me a ping to click the project link and take a peak at what happened the day before. It works OK, but not ideal.
7. Hack the companies. Once we purged the clients out of Basecamp, we realized that "Companies" are the secret for organizing projects by phase. We had struggled with this for over 2 years, since Basecamp likes to organize projects alphabetically by Company. You can still use client companies if you need to, but the follow will help you organize projects the way you want to see them.

How to Organize the Dashboard by Phase:

This tip uses the little known "File under this company" drop down (Well - I was ignoring it for years). This gives you a list of all the companies you've added to a project on under "People & Permissions". This is handy for organizing a project that has multiple companies on it.

First, create a number scheme of how many phases your projects have. Here's mine:

[1.1 First Phase]
[1.2 Next part of that phase, if it needs to be tracked]
[2.1 Second Phase]

The numbers don't really matter, so long as they are sequential. This makes the phases in order when Basecamp alphabetizes them on the dashboard. I added brackets to the names; it just looked better to me. Add these companies from the Dashboard > "All People".

As of now, you can't automatically add your project phase/companies via a Project Template (only your company/people). This is a shame, but it takes 2 minutes to add them all when you setup a project. This time is well spent getting things setup at the start.

Now, when a project moves from phase to phase, simply change which Company it's filed under on the "Project Settings" tab. Your new dashboard will list out each phase, with the project names underneath. Pretty cool, huh?

UPDATE 2/1/2010: Maximize Project Templates:

The "Hack the Companies" tip works well when Basecamp is accessed primarily from the web interface, often in a desktop environment. Unfortunately, it's not so friendly for Basecamp Extras & Add-ons mobile apps or 3rd party applications like ProofHQ.com (SpinWeb uses it to colloborate with our Web Designers for design revisions). In this case it's best to use the traditional company setup for clients, with micro sub-projects for project phases. At the request of a few team mobile workers, I changed our system to focus on project phases.

1. Setup Project Templates for phases. At SpinWeb, we split our projects into 5 phases (Blueprint, Design, Deploy, Build, Launch). Each phase is independant with it's own timeframes (Building a site doesn't start until the Design is approved).
2. Sliding milestones. Separating project phases is great for using the built in "Shift future milestones too?" feature. Start with the first milestone in the series, and you can move the whole gang with a few clicks!
3. Space your milestones in advance. The best feature of a Template is that you setup Milestones, To-do lists, and assignments in advance. Use the sidebar calendar grid to see how your timeframes stack up.
4. Link your To-do lists to the Milestones. 

Within a few minutes, you can have a pre-populated project that use your best practices. Update your template often to keep inproving each new project. 

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