While I haven't ruggedized an arduino, I used to work in a telemetry company and have ruggedized bespoke integrated kit for use in hazardous + very rough conditions, and these few tips from past experience came to mind.
Potting: once your board is tested, put it in a small appropriately sized tray and fill with potting epoxy. for bench prototyping, at a pinch you can use candle wax (but NOT for field, heat can cause wax to vaporize and become fire risk). pro tip: remember that the viscosity of your potting compound changes with local ambient temperature, so always test one board before doing a batch or you may wreck a lot of kit (epoxy will either not fill into all areas, or will be too thin and seep into connectors)
Cable bleed: both sides of cable shielding must be properly sealed. liquids seep through cable shielding and can cause big problems.
Enclosure: If heat is an issue usually using a metal finned enclosure for the device will wick away enough heat. If power usage is no issue, you can use a TEC to assist. When sealing, always use the right kind of sealant, some sealants release vapor that will corrode copper over time. Also, use marine-grade screws in field if you don't want to have to use a drill to re-open it later.
Connectors: we had a lot of joy with the Bulgin Buccaneer range. They aren't perfect in high pressure rapidly changing temperature environment though, we had to pot them after installation for best results.