Well, obviously for me, I've got a fair number of German and British ships in 1/2400. Primarily WW1 stuff, sourced from GHQ (capital ships) or Panzershiffe (cruisers and DDs). I also have about 80% of both the US and Japanese OOBs for Midway (Japanese CVs converted and painted to be correct, damned left-side islands) in that weird 1/1800 scale that Axis&Allies War at Sea used. I don't have nearly enough planes for 7 CVs, though, and I'm missing the Japanese BBs and MAYBE one of the US carriers (they've been boxed for a few years now, I can't recall).
Rules-wise, I favor General Quarters 3: Fleet Action Imminent. I also have a homebrew system I've been toying with that allows the player to custom-build their own ships if desired. The homebrew (Gratuitous Battlewagons v0.2) is intended to allow the player to control 1-4 capital ships and actually make them feel like ships; most systems which aren't Harpoon! or Seekrieg reduce ships to a small stat block and a "blob" of health. It's actually very similar to Alpha Strike vis a vis BattleTech. The problem is that the naval games on the "BattleTech" end of the scale are so complex as to be almost unplayable...which is a whole different issue. Gratuitous Battlewagons is intended to allow ships to be fought in detail and take damage in detail while still being reasonably playable.
Travis, are you going to be there tomorrow? I'll bring a printout of the GB rules, if you'd like to read them.