As mentionned before: this highly depends on personal preferences. I think I have one of the biggest colelctions in quantity of cards. However, in quality my collection is by far inferior to those of the more experienced players. For example, I think I own about 50 or 60 Bang Nakh - Tiger's Claws, a card nobody ever uses.
I have divided my collection in several groups in the way I believe I can reach a certain cards in the most efficient way.
1.) Crypt cards (by far the largest group): I have them sorted by clan, then by group, then by capacity and only then alphabetically. I find this the easiest may to do deckbuilding.
I have the luck to own every crypt card at least once (For the record, I'm still lacking about 70 cards to own them all at least twice). So I have 2 binders (1 with cama, caitiff and sabat-clans (including antitribu) and the other with independant, laibon, bloodlines and imbued) which include 1 copy of every crypt-card. They are sorted the same way as the crypt-collection. I added a number in front of some cards, usually stating how much copies of that certain card I lack to get up to 5 (In some rare cases, I want more than 5 copies, for example aabbt kindred, tupdog, annabelle, anarch convert, cybele ...). So a card with number 3 in front of it is sought after 3 more times, meaning I own 2 copies of the card already. This may seem a strange way of numbering them but it works for me.
I always browse those 2 binders when making new decks. It also tells me exactly where I can find the crypt-card in question, since the binder and collection were built in the same way. I've only once used a card from my binders in a deck (Tupdog for the tupdog-deck). To be thourough, I have to clarify that I still haven't found the time to include the crypt-cards from unaligned or storyline rewards into my binders. I really hope to get this done before the next set comes out.
2.) Masters: They are divided into several categories: discipline masters, regular masters (no clan req.), clan req, trifles, archetypes and trophies. Each category is sorted alphabetically.
3.) Events: They are in a single box and sorted alphabetically
4.) Discipline cards: they are sorted by discipline and then alphabetically. I do not make a subdivision between action, action modifier and reaction, since a deck with a certain discipline will like have all types of cards (e.g. a deck with dominate will often pack govern, conditioning and deflection). I find it easier to deckbuild this way.
5.) Clan req. cards: sorted purely alphabetically. No subdivision between the different clans is made, since I don't own that much clan req. cards.
6.) Political actions: they are divided into 4 categories: no req. (by far the largest group) and req. (like parity shift or dogs of war, firebrand...), crusades and praxis seizures (since the last 2 groups contain quite a lot of cards and are only used in very specific decks). To clarify, I don't consider a cost of blood or pool to be a req. Each category is then sorted alphabetically.
7.) Non-political sect req. cards (2nd tradition, reunion khamut, but also seraph's second) are sorted by sect (cama (or prince/justicar/...), anarch (or baron), sabbat (or bishop/black hand/...), laibon (or magaji) and then sorted alphabetically. Again, I do not make a division between card type.
8.) Cards requiring 2 disciplines are stored seperately in alphabetical order
9.) The 3-discipline anarch-cards are sorted seperately in alphabetical order
10.) Equipment is divided between no req. (like .44 magnum or bowl of convergeance) and req (like Erebus Mask or Femur of Toomler). Again, I don't consider a cost of blood or pool to be a req. Each category is then sorted alphabetically. Thinking about it, have to clarify that a card like Kduva's Mask is stored with the cards foubd under point 7.
11.) Allies: They form a seperate group and are sorted alphabetically.
12.) Retainers: They form a seperate group and are sorted alphabetically.
13.) Imbued: I store everything that is specifically imbued in a seperate box. This is further divided into the following categories: crypt cards (yes, those are not stored in group 1), masters (angel of berlin and church of vindicated faith), action/power + action mod + reaction + combat, eqpuiment (crusader sword and Living Wood Staff), ally (Moise Kasavubu) and convictions. The crypt-cards are sorted the same way as done in point 1 (by 'clan', then group (irrelevant here), then capacity then alphabetical). The other categories are sorted alphabetically. The events are put in group 3, since none of them require you to actually have an imbued. They could technically be played in any deck.
14.) Cards without req.: are sorted between action, action modifier, combat and reaction. Each category is then sorted alphabetically. The same goes here: I don't consider a cost of blood or pool to be a req.
15.) The "unopened stuff": I do have some unopened boosters & starters from severals sets. I don't really consider them part of my collection just yet, since I don't always know what's inside. Lacking space, they are even kept in a different closet.
16.) Lastly (I think), I have a box of "unsorted cards", since I have the bad habbit of not putting the cards immediately back into their place after building (or breaking up) a deck. So when the 'unsorted' box gets to full, I take the afternoon to sort out the box and put the cards back where they belong in the collection. Most often, I have a vague idea what cards are in the unsorted box. So it happens that instead of going into my collection to get a card, I pick it back up from the unsorted box. This is escpecially the case for cards used in a lot of different decks (pentex, on the qui vive, target vitals ...)
I realise I made a lot of different groups, but I find it allows me to find a specific card relatively fast. I use ARDB for my crypt-collection, since there I have a clear target of how much copies of each card I want. For the other cards, it's much more difficult to say how much cards you actually 'want'. The more the better, seems to be the philosophy.
and though We are not now that strength which in old days
Moved earth and heaven; that which we are, we are;
One equal temper of heroic hearts,
Made weak by time and fate, but strong in will
To strive, to seek, to find, and not to yield.
I have a more reduced collection both in quantity (approx. 2500 cards) and in quality but I sorted it out like this :
One box with crypt cards sorted by clans ( I followed the order put in the little memo cards in the starters, so they are grouped by sect also) and alphabetically per clan.
The library cards are sorted in groups : without requirements, with sect requirement (Camarilla, Sabbat, Independant, Anarch, Imbued in that order), with clan requirement (sorted by clan), with discipline requirement (sorted by discipline).
In each group the cards are sorted by type (in the order they are played : Masters, Actions, Modifiers, Reaction, Combat, events)and alphabetically in each type. The cards requiring more than one discipline or more than one type are sorted at the end of the type or discipline.
that let me find quickly a card knowing what it does or search a limited number of cards if I search cards with a special requirement (e.g. anarch cards or cards requiring dominate).
But I only used some piece of paper with the name on it (e.g. "Malkavian" or " "Dementation").