I don't do a lot out tweaking on acoustics beyond adjusting the action but I did add a Hipshot D-tuner to my old Lowden which very quickly and accurately will move the low E to D and back again. It comes in handy when backing tune players and you want to switch from standard to Drop-D during multi-tune sets.
On my MIM Fenders, a tele and a strat, I've installed Lindy Fralin pickups and new wiring harnesses, made a world of difference.
+1 on Waverlys and K&K under the bridge plates but my I also have a LR Baggs Lyric mic that attaches to the bridge plate in one of my instruments that's as good as any acoustic PU I've ever heard.