I drive a fair bit off-road (about 2,000km in the last 10,000), completely stock--rocky and often muddy terrain. With adjustable air suspension, I never felt the need to do any modifications. I've been thinking of getting protective aluminium plates Touareg Expedition-style to for extra peace of mind on gravel roads but didn't get around to it. Ideally I'd want a snorkel (or two) but as nooby said there aren't any after-market parts and the snorkled Touaregs on google look really ugly (must impede visibility also).
My only problem is my 19" wheels--the massive torque in Low4 on rocks kills the tyres. I've destroyed two tyres with tears in the sidewalls. The fist time I'd reduced tyre pressure to around 38psi and decided to go over a log lying lengthways at the edge of the path (to avoid a 1' wide and rather deep ditch half across the path--this was in early days before I realised advantages of independent suspension) and the gnarly protrusions on the log literally ate away bits of my sidewalls. The second time, I didn't deflate the tyres (44psi on AT tyres) and decided to drive down a rough path which had a lot of rocks washed on it during the rainy season, steep downhill (3,000m to 2,400m) in Low4 and again some rock slashed the sidewall of another relatively new tyre. Now I avoid putting her in Low4 on rocky terrain.
(FYI I have General Grabber ATs--very good in mud but I think very poor sidewall quality compared to a Land Cruiser equipped with Kevlar reinforced Wranglers I occasionally get to drive--or perhaps short sidewalls and massive torque are more to blame than General tyres)