As mentioned, E46's have a relatively tight engine bay and may require you to remove stuff in order to get to whatever you need to replace/repair. This is generally not that big of a deal.
I highly recommend you purchase a car with a full/good service history. I'm talking regular oil changes, common repair items taken care of, and a car that looks to be in good condition.
Some of the common issues with the E46 are failing window regulators, tail lamp wiring faults, the cooling systems have been known to be iffy (failing water pumps/failing radiators), VANOS unit failure/wear. Most of these issues would have more than likely been repaired by BMW during it's warranty (you will be able to determine this by the vehicles service history).
All of the above are relatively minor when compared to subframe failure which plagued the E46 chassis. However, BMW recently settles a class action lawsuit which means they will repair any damage that might occur. The repair kits for the subframe essentially involve welding on a reinforcement plate. Not all E4's suffer from this but it has been known to happen.
There's a really nice Wiki at Bimmerfest that has a ton of information about the E46. It is arguabley the most popular BMW ever produced and it is a fun car. Click here
I will say one of the nicest things about the E46/3 series in general is the mass amounts of upgrades that can be done to them. There is a lot that can be done in terms of cosmetic and performance upgrades.
Best of luck finding your E46 and if you have any questions shoot them our way. I'm sure someone will answer whatever your question you may have.