To keep track of things in the boat as well as those things which reside in our California storage unit and our Maryland storage unit, we've done a couple of things.
First, regarding the storage unit in Maryland (long, long term storage of furniture, household goods, files, family stuff) I made an inventory of each box/bin and numbered each box/bin, then made a diagram (and took some pictures) of the storage unit in Maryland so that anyone can retrieve an item for us. We also inventoried items like skis which didn't fit into a box by putting a sticker on each item. I learned this trick from the days that hubby was in the Navy and we were stationed overseas--we knew that we could ask for items to be retrieved from our storage unit if we could properly identify the items by their inventory stickers so they could be sent to us.
Our California (local) storage unit and the boat are done differently. In these cases, I am the ship's "quartermaster" keeping track of where things are and so forth. I luckily have a very good memory for where things are placed even as they're moved from spot to spot. This served us well with our our Navy moves as I could really remember what was in each box even after it sat in storage for years--without looking at the inventory list. So it really isn't too hard for me to recall what is placed where throughout the boat and in storage. The boat is more difficult because often things are placed based on weight and shape to fit a particular location rather than by any type of useage logic, though.
Lists and pics are great. I tape little lists of what is in a locker on top of the locker so that hubby knows what is there.
When I'm here--David just asks "where is such-and-so" and I can usually rattle of location immediately. In addition to lists, to enable hubby to find things without me, I do also take many pictures of things as they are going into the lockers and storage areas and we have a file folder on the computer with the pics and hubby keeps a copy of that picture folder on his little Nokia N810, too. Since much of our in-boat storage remains to be built, we have several large net "retaining walls" with stacks of our stores in duffle bags behind the net walls. These duffel bags are various sizes, various colors, and are organized by project area or tool type. We can tag the bags or write (with sharpie) on them as to the types of things inside them. Adjacent the engine compartment, for example, we have three large duffel bags strapped to the bilge stringer segregated into "general boat parts", "plumbing", and "engine/genset parts" In another location we have an electrical duffel bag and an electronics duffel; the former with wiring, extension cords, breakers, etc, the latter with the multiscope, ttl parts, radio and computer tools/parts and so forth. Sometimes these duffel bags are way too heavy to lift--the rigging one is strapped to a bilge stringer in the stateroom and couldn't be moved without removing extra rigging screws, toggles, and other stuff from it.
It doesn't take a whole lot to keep track of things as we do. I must say, though, if something is truly an unneeded item, it tends to be buried and I do have a little tickler list of "items that we really don't need but are here on the boat just in case" Those items are actually hard to keep track of but are VERY important. They're typically raw materials--steel plate, bronze rod, wood backing blocks, etc.
Food. We have a layered approach similar to what others have mentioned. I grew up in with parents who grew everything we ate and canned it/froze it/smoked it/whatever. Given that we always had huge amounts of food around at all times, I'm still not comfortable unless we have what is always more than a month or two of food in my pantry. So, I'm a major food-stasher here on the boat. Some of it in out-of-the-way locker space and some of it readily available in hanging nets and duffel bags. So far it works n regards to storage, but I must admit that it is almost impossible to use our galley while underway since the galley is not fully complete and I don't have a good means of wedging myself in place while preparing food. On the short trips we've done so far, if it is rough, I've literally sat on the galley sole with my 2 ft x 14 inch cutting board as my "countertop" on the floor for food prep. The stove, luckily has good built-in fiddle rails around it so it (or the alcohol stove which can sit atop it) can usually be used unless things are really, really rough.
I know it is better for folks who have a "complete" interior to their boat, but I never dreamed I'd be spending so much of my time crawling around on the sole digging things out of duffel bags while the boat heels and rolls.