A few simple methods work well for speedlight gels:

• Keep only the gels you actually use, then preserve the paper labels/spec sheets so you can still identify each one.
• Remove the original fastener and put the remaining gels on a small carabiner-style key ring through the existing holes. This keeps them together, easy to flip through, and hard to lose in your bag.
• For better protection, store loose gels in a small case or pouch with separate slots. Some photographers repurpose memory-card wallets for this and label each pocket.
• If durability is the main concern, laminating selected gels together with their specs can make them tougher to carry and sort.
• Another option is buying a pre-cut gel kit that comes in a compact plastic case.

In practice, a ring for quick access or a small card wallet for better protection are both solid solutions.