Reaper doesn't technically have any mono channels. Each channel has a minimum of two parts, making it stereo. This caused me no end of confusion when first using mono AU plug-ins with Reaper.
The problem is that when you use a mono plug-in, it only affects one of the two stereo parts, so the result is a mix that's nicely EQed and compressed in only one ear. If you're experiencing the symptom of mono plug-ins making mono recordings strangely become stereo all of a sudden, this is probably happening to you.
Thankfully, the fix is quite simple. Click on the FX button to bring up your plug-in, then click on the button labelled "1 in 1 out" or "2 in 1 out". Click on the lower right square so that the plug-in's single output goes to both parts of Reaper's stereo channel.
The hard part is that you may just have to EQ and compress all your mono channels all over again, now that you can hear them properly...
VST plug-ins seem to have this sensible routing by default, but AU ones don't seem to have it yet. So for now, I'm switching over to VST, which seems to be more efficient on my computer anyway.
By default, scrolling horizontally with a Magic Mouse in OS X in Reaper will make it scroll in the wrong direction, and scrolling vertically will zoom. Let's fix that.
Go into Actions > Show action list (or type in a question mark as the shortcut). This intimidating screen is where Reaper keeps track of which actions perform which tasks.
Type in "mouse" for the filter, and scroll all the way down. These are the bits we're interested in.
For the "description" (task) of "View: Zoom horizontally", remove the "shortcut" (action) of "Mousewheel". That stops vertical scrolling from zooming in and out.
For "View: Scroll view vertically one page", add "Mousewheel". (Click on the Add button, move the cursor over the new window, and actually scroll vertically. Click on OK.) That makes vertical scrolling actually scroll vertically.
Similarly, remove "MultiHorz" from "View: Scroll view horizontally one page reversed" and add "HorizWheel" to it. This makes horizontal scrolling work in the right direction.
If you're using subtle effects on every channel — say, tape and mixing desk emulation — it's useful to turn all of a project's effects on and off at once to hear the aggregate difference. You can do this by going into Preferences > General > Keyboard/Multitouch > Assign keyboard shortcuts to actions or change existing shortcuts. Find the description "Track: Toggle FX bypass on all tracks" (filter for "bypass" and scroll to the end — it's the next to last one). Select it, and click on "Add..." to assign a shortcut for it. I chose a letter B for Bypass. Close the window, click OK to the preferences, and you're good to go. B now toggles every effect in your project on and off.