I have a big roller box that I like for the longer trips, a Predator large size that cost $150 from Outkastfishingtackle.com. It holds three of the Plano 3700 trays plus an oversized 3730 tray in the main body, and I put another 3700 and a 3500 in the top tray, plus deckhand kit and stuff. I took the rod-holders off of both sides and use the side panels for other things. Has held up well for four years and still going strong. Since it is going to sit up on the top of the tackle rack I also secure it with a bike lock cable so that it doesn't tip over in a boat roll.
The only issue with a big box or bag is getting a spot on the boat so that you can get into your stuff without being in everyone else's way. So I only take it on the longer trips. For 1.5-day and less I use a nice bag from Flambeau called the AZ6. It carries six of the Plano 3500 boxes, although I only use 5. The extra space holds a water bottle and my deckhand kit and such. I load the boxes vertically so that I can get into whichever one that I want easily. It has a waterproof bottom and useful pockets all around, and comes with a carrying strap to help if you load thirty pounds of lures and stuff like I do. The zippers are strong. It is a well-made tackle bag for about $50.
I replaced the tackle boxes that came with both the Predator and the AZ6 with better boxes that were in different interior designs and had better plastic latches.