1) Scanner type - 1D (linear barcodes), Imager (linear and 2D, including QR-codes), Omnidirectional (reading from any angle, ideal for retail)
2) Connectivity - wired (USB and/or Serial ports), wireless (Bluetooth, base station/dongle)
3) Environment - indoor or outdoor; regular or durable (rugged case)
4) Scanning distance - standard-range (retail), medium range or long-range (for example warehouses).
5) Other specifications like ergonomic design, scan rate, budget, brand.
Read more about choosing barcode readers from here.