There’ Magicshine MJ-818 out there. Very bright (85lm of red light is a lot) and small light but uses 4x18650 battery pack (shared with front light), I think it uses 8,4V so you could just hack 2x18650 holder for it. Many reviews posted online. Not cheap and probably an overkill for most situations.
If you are willing to mod something you could adapt BlitzWolf BW-LT5 for tail light - it’s self contained and has steady red and strobe modes, just needs some kind of mount to fix it to the bike. BlitzWolf BW-LT3 is currently on sale for $6.99 but only has white LEDs so needs swapping those with some red SMD - piece of red LED strip should do fine(sans resistors), but don’t know if there’s current regulation, so you may need to connect 2 red strings in parallel . It’s actually quite easy - here are the pics: BlitzWolf BW-LT3. You can even change 18650 to whatever capacity you like. Only downside is not easily accessible cell for swapping on the go.
This Warsun H006 has swappable cell but unnecessary (in that application) white flashlight
Another route would be building something using this board: $0.99 charging module with cell protection, provided you can hack together some enclosure. You would have USB charging already built in as well. One cell holder, red led strip, some wire, resistors and you are good to go. These cell holders look good:
http://www.ebay.com/itm/2Pcs-Open-Frame-Plastic-3-7V-18650-Battery-Holder-Case-Cell-Box-Black-/321433137283
Do not but the cheapest stuff with coiled springs as those break easily and are inferior quality.
You could just as well buy any one cell constant current LED driver and slap some red XP-E or any other power led (< $2) and you will have blinding monster exceeding abovementioned Magicshine for fraction of the price.
But other thing to consider - those 2x0,5W power led tail light running on 2xAAA are quite powerful and blinding. Red leds use lower voltage than white that translates to less power so those lights will run quite long. Serfas USL-TL60 or Moon Shield (same thing) lights are also worth considering if you want brightest tail light. But those are USB rechargeable with built in prismatic cell. Those are expensive but very compact, light and powerful.
So it really boils down to your preference and expectations - options are numerous but we will probably never see abundance of 18650 tailights as prismatic cells are better suited and adequate for that application (self contained light) and high current 18650 is simply an overkill and would only contribute to bigger enclosure and mass.
EDIT:
I use Smart Superflash (first version 0,5W, it’s PBSF Superflash rebrand) since maybe 8 years and still going strong. Two eneloops last me whole season. It’s declared it works for 190 hours in flash mode. Since then many variations/clones emerged including 1W version which is brighter but runtime still aroud 100h in flash mode (30h in steady). This $3 2x 0,5W light is worth checking - claims up to 60h in alternating flash mode, 30h in double flash and 15h in steady. It’s sold under many expensive brands even for more than 30$ (see for example Portland Design Works Danger Zone), I really doubt the LEDs are different. Should work fine on eneloops as well and two spare cells in case you want peace of mind takes up virtually no space.
Some reviews here: http://www.dx.com/p/bike-bicycle-3-mode-red-light-led-safety-warning-signal-lamp-taillight-black-red-2-x-aaa-337694#.Vz7ZC-Td3bj
If you ride in rough terrain mounting may need some better securing.