Minecraft wiki entry for Navigation, associated text: Maps: Very useful in navigating large oceans. Zoom them out to avoid ending up with an entire map covered in blue.
Jack-o-Lanterns: Can be placed underwater and oriented to show the direction home.
Lily pads: Can be placed down to form a trail. Can also be used to make small lava islands. Place the lily pad, then use a lava bucket on top of it. This forms a stone island with flowing lava. If you remove the lava, the island can be used as a mini-base, having enough space for a chest, crafting table, and even a bed.
Towers: Built from the seafloor to well above the surface, and topped with a light source. Glass blocks or panes also carry light into the depths.
Additionally, consider shaping the waterways, adding canals, and/or constructing a lighthouse to show the way to shore.