Found it! Its a little work but check out the screen of the final product - beautiful!
http://blog.jailbreaksource.com/?p=762
Awesome. A little too ripply if you ask me, and arguably doesn't go with the TF2 theme so well, and it has one of the same problems that effects/water_warp had, of appearing to move more at greater distances. Maybe someone here who has a better grasp of how this works can refine it into something that matches the game's default underwater effect. Possibly using one of the built-in water textures as the base.