I've yet to purchase a car of my own, but being in the market for the past several months I've compiled a decent amount of advice from various sources.
As for your pick, I can say Honda = Good, Aftermarket Modifications = Bad. Hondas are great. All my friends with Hondas hold them in very high regard, and Honda's popularity is no coincidence. However, cars with aftermarket parts are harder to maintain - nonstandard parts means nonstandard service. And, you have to consider the type of driver who would bother to modify their car; an enthusiast, someone who has probably pushed their car to the limit. Car-types are great people - they're typically very knowledgable, skilled and friendly - but chances are that their used vehicles have seen a lot more wear and tear than your average commuter car. This is not to say never buy such a car - just be aware, ask lots of questions, and make sure to have the vehicle thoroughly checked by an expert. $100-$200 to have a mechanic look it over beforehand is a lot better than the thousands you could have to pay to fix a lemon.
Or worse, you could be getting a car from someone who just wanted it for show and did a cheap installation to add flashy, expensive parts. This happened to a friend of mine - he bought a Prelude at a decent price with a nice custom stereo in it, low mileage, ran well for about a week. Everything but the stereo was factory, and the stereo apparently worked well enough when the seller demostrated it to my buddy. But one day he tried turning the stereo all the way up and poof! A hacked wiring job to power the subwoofer shorted out most of the electrical system and burned a big hole in the upholstery, not to mention ruining the stereo. Total cost, after paying $6000+ for a mid-ninties Prelude: something to the tune of $2000 for parts, an upholstery kit, and a new stereo. All of the repairs were done by my friend and his family - fortunately they were all mechanically inclined and had a garage full of auto tools. I can't imagine what it might of cost had he taken it to a shop.
So be wary! Find a friend who's good with cars and have them coach you on what to look for and ask, or take them along and just have them do the talking for you. I have a very tall, intimidating roommate with a decent working knowledge of cars who saves me a lot of time at auto dealerships.