I've recently completed a long, complicated piece of character animation, and I really made extensive use assigning layers to goals/control objects. With a little bit of front-end set up, you can make a really nice rig that will be a breeze in the Timeline editor. The main things to take advantage of here are:
LAYERS: Judiciously assign layers to obvious groups, like Body/Arms, Legs/Head, etc. You can nest layers within layers too.
SELECTION OBJECTS: Create any number of selection objects containing only those controls you want to select and key. These then show up under the Keyframe Selection button, next to the Auto and Manual Keyframe buttons (the Red circle with the "?" inside). You can select any of the sets, and restrict the selection of objects in the viewport and auto-recording of its keys in the timeline.
LOCK ANIMATION: In the timeline, if you only want to record keys for, say, the Z axis of a rotation, assign a specific layer (calling it something like "Locked Tracks") to the X & Y tracks in the timeline column and click on the padlock icon in your Layer Manager. Now when you rotate a control, only the Z track will record, saving you from inadvertently recording the others.
BOOKMARKS (under Timeline Editor's menu): Super helpful for switching between saved sets of cherry-picked object(s) and hierarchies in the Timeline. Alleviates a ton of hassle and really streamlined my workflow.
I've also found taking snapshots of my F-Curves helpful from time to time when doing some surgical-level tweaking, and I also like to display the color of the layer for the object's tracks in the timeline (under Timeline Prefs). Helps to distinguish visually (as well as the axis colors). Anyhow, on top of the rest of the suggestions up thread, adjust to your tastes of course. There's some hidden workflow power in there, it's just uncovering and applying it all that's a bit elusive.