I won't say what to put in each bottle since exactly what fits will vary. I would probably distribute items among bottles so you could get by with one bottle or a small number of bottles. I.E. distribute your redundant items among bottles instead of putting all your eggs in one basket. Suppose you have a dozen bottles, 4 each A, B, and C. If you have one each of A, B, and C you have a rellatively complete kit and even with only one of A, B, or C you may have a useful kit. Thus A might be big on water purification and B and C have weaker options, etc.
Typical nalgene bottle dimensions: 3 1/2 Inches Diameter, 8 1/2 Inches tall, 63mm neck.
usual first aid kit, fish hooks, fishing line/paracord/wire, etc.
Sawyer mini water filter. Cheap, small, Fits standard soda/water bottles, squeeze pouches (1 included), or hoses, filters far more gallons than the frontier and remove more bacteria. However, probably even less effective against chemicals. Should fit inside nalgene bottle.
Iodine as a backup, for first aid, as a disinfectent, and to mitigate exposure to radioactive iodine. Separate container from sawyer mini. Also, other disinfectants.
Bleach, calcium hydrochloride, alcohol gel, etc.
Pictures of dead presidents, junk silver, etc.
Ziplock bags, trash bags. To store things in, protect from water, carry water, and dispose of waste. Large trash bags also work as a temporary shelter (an old caver trick). Every bottle should probably have at least one of each. And maybe one of the sawyer water pouches.
Space blanket.
A lighter or other fire starter in each bottle.
Distributed over separate caches:
NAA .22LR or 22magnum mini-revolver + ammo.
pepper spray
Folding one-hand open locking stainless 2.9" knife.
Swiss army knife
Multi-tool
Knife/fork/spoon, spork, etc.
First watch door lock. Positive action, Does not rely on friction jamming latch and less expensive than addalock but slightly heavier.
http://www.amazon.com/First-Watch-Temporary-Interior-Security/dp/B005409JNU/ref=sr_1_12?ie=UTF8&qid=1389761765&sr=8-12&keywords=addalock
Water bottle carrier belt, sized for your nalgene bottles, stuffed inside one.
An aluminum soda can is just about the same size as the neck on a typical quart nalgene bottle. Not sure if it will fit inside or not. Think pot. If it doesn't, there is always the fine art of metal spinning. Beware of plastic linings. I would point out that you can get aluminum water bottles at the thrift store for about the same price as the nalgene bottles although you should avoid direct contact with dirt unless you copper plate them.
Soda can alcohol stove. Rubbing alcohol as a fuel and first aid prep.
An esbit stove is a little too big, but the pellets aren't. Emberlit stove could possibly be bent to fit.
eyeglass repair kit, if applicable.
Flashlights
candles
burner phone - depends on the situation you are preparing for but there are a number of situations where your personal S--- hits the fan and you might not want certain people to find you.