Take Sunbird. The source tree is organized as a set of backend modules, with various products including as many of them as they need and then throwing up the main frontend window on top (although SeaMonkey really has diverged its UI in quite a few places). Sunbird was the standalone calendar app, but it was decided that the calendar maintenance team was too small to maintain a standalone calendar and instead shifted their UI focus to only supporting SeaMonkey/Thunderbird integration (aka the Lightning extension). No code that actually did anything was removed--I was the one to actually hg rm it here: https://hg.mozilla.org/comm-central/rev/f2e605ee5475
As you mention, MXR was phased out in favor of DXR, which is itself being phased out in favor of searchfox. (I too worked on DXR, back in 2011). Prior to MXR, there was LXR (as in, lxr.mozilla.org), but I'm not sure it's worth mentioning as a separate project since it's basically an unmaintained fork of the LXR project.
While we're on the topic, there's a lot of "missing" webspaces here. Bonsai was a webtool to display atomic CVS commits, Tinderbox was the UI for seeing if the tree was broken (on fire) or not (this later gets supplanted by TBPL (tinderbox/pushlog), itself rewritten to not be a pile of hacks as treeherder), and there's definitely a buildbot clone/fork/I don't know floating about somewhere in the mix.
There's various versions of things like the addons website or support websites that I can't even enumerate off the top of my head as well. Some of these (like old addons stuff) was completely in-house, while others (like pastebin and etherpad) are hosted versions, potentially with some modifications, of other projects. None of these are listed, but do they even deserve to be listed? It's not consumer-facing, and I'm sure even many Mozilla developers would struggle to realize some of this stuff existed.