A couple of bad mods:
Trail Master Exhaust on a Nissan Hardbody PK back in the day. It was essentially a "Y" pipe after the catalytic that sent the exhaust through two glass packs. The exhaust was all stainless, but really loud, the kids today would have loved it, but nothing stealth about the set up.
99 TJ - Not changing the gearing soon enough. I have been running 31x10.5AT Tires on the Jeep for 8 years and never changed the gearing. I changed the diffs last summer,to 4.11 and its fun to drive again. I can actually use 5th gear. Should have done this mod years ago.
As for the roof rack - I think its essential on a Jeep. I have an "East Coast" rack that can be installed or removed in 15 min. Put my rocket box on it and the jeep actually has a trunk. Hate the rack without a load due to the excessive wind noise.
My other gripe is that many aftermarket companies do not make their products to last very long. The paint and finish is not designed to last the life of the vehicle. I tend to keep my vehicles a long time, and I don't want to keep replacing items like bumpers. My TJ has over 177,000 miles on it and is still running strong, and the Olympic Rear bumper has look like crap for 150,000 miles, while the OEM front bumber is still looking good.