What causes The HOM effect and how can you get rid of it? Thanks.

The most common cause of HOM is too many adjoins in view of the player. The engine limits the number that can be displayed at once to a hard-coded number, so when you reach that number, it simply doesn't render the areas where the HOM effect shows up.

What this means is if you have a really complex area, you're likely to get HOM. You'll have to tone down the detail a little bit. You could use some custom 3dos to take the place of the more complex architecture, or you could carefully plan the geometry so you can't see as many adjoins at once.

Or if you do a bad cleave job or somehow delete a surface so that you are looking at 'nothing' you shall see HOM.

A patch has been released that raises the adjoin limit, so there's that alternative, too (granted, everyone who plays your level will need the patch to get rid of the HOM, and framerate may be low if a great many adjoins are present...)
But, then again, 3dos are easier to edit if you mess up/need to revise...

Also, to find such surfaces that Axis has described, you can use the following params in the Ctrl+F dialog:
Adjoined Surface [is not] [-1]
Geo [is] [0]

Also, if a surface in your level is not flagged as "impassible," it will be passable and if you touch it I bet you get the HOM effect.
I've also had it sometimes where a sector was assigned 0x1000 (collide box) when it shouldn't and gave me some weird effects when trying to walk through it.