Trays are one way. Another is 35 mm film cans: if you're shooting clips of 35 mm film, just curl the film, emulsion in, into a film can. Even a translucent one, just fill it in the darkroom, put the lid on to agitate, and once you pour in the fixer, you can turn on the light (some folks suggest giving one minute in the fixer first, your choice). If you've got a bunch of them, you could tape them together as you feed them in to a plastic reel for a daylight developing tank.
For anything larger than 35 mm, yep, trays.
