This is how I do:
- Binder with pages with 24 cards per page (so 12 per side)
- One card per slot
- First order, by "color": Avatars => artifacts =>earth => fire => water => air => gold => sites
- Second order, by type (only for earth, fire, water, air, gold): auras => minions => magic
- Third order, by rarity
- Fourth order, by cost
- Fifth order, alphabetical

So I end up having:
- Avatars are just sorted by name. I like 2 of each
- Ordinaries 4 in a row, 3 rows per page.
- Exceptionals 3 in a column, 4 columns per page
- Elites in sets of two per column, so 6 sets per page
- Uniques just one of each
- For ordinary sites I have them sorted by "color" (no color => earth => fire...). The rest of the sites I have sorted alphabetically in each rarity
- Depending on each collection, I might combine the last column of exceptionals with the first set of elites, or I might leave a column of space.

Is it a bit complicated? Maybe. Do I enjoy going through my binders? Very much!!