I am going to go ahead and toss some things out there that I know have been a point of contention about for a long time.
MUSICAL INSTRUMENTS. Yes, there are those "hard liner" CofC types who claim that there is some sort of biblical justification for acapella music, and I suppose that if you really stretch things, there technically isn't a mention of a musical instrument in the assembly in the NT. Some stick with that. But if you look at CofC history a bit, going back to the Civil War, the lack of pianos/organs in the CofC was more of an economic decision: The south was decimated post war and many of those CoCs simply had no money to buy or replace an expensive instrument.
Later the CoC would split - the Disciples of Christ (DoC) kept the instruments, and the CoC went without. So if you look at the footprint of the DoC and CoC, you find that most DoCs are in the north, most CoCs are in the south. And there are a number of CoCs in the north that do have instruments, and more and more in the south that are adding them.
This isn't a doctrinal issue except for the ignorant and dogmatic. It's really more of a tradition. I am take-it or leave-it on the issue.
COMMUNION. Yes CoCs typically take communion every Sunday, but that's really just following the pattern of the early church. Acts 2:46, "When they came together, they broke bread." Of course, this scripture might or might not be the holy communion, but it's just something CoC follows. But not to the letter: CoC has Wed. night services (and other meetings at the church) where there is no communion. Of course, Jesus said "Do this in remembrance of me," so CoC does it every Sunday. Again, only the most ignorant and dogmatic would claim this to be any sort of deal-breaker for anyone (although I know those types!).
BAPTISM. This is the biggest difference between southern Baptists and Church of Christ. And it boils down to this question: Are you saved before or after you are baptized? Quite honestly, there are strong, well-thought-out lines of thought on BOTH sides of this issue. BOTH denominations place a high priority on baptism. But for the Church of Christ, once you decide you want to become a Christian, it's more of a 5-alarm fire (no pun intended) to get to the water. In the Baptist church, it's all good, wait until baptism Sunday. I don't condemn the Baptists for their line of thinking, because I fully understand it (baptism isn't a work).
But I am personally a bit MORE COMFORTABLE with CofC on the issue, for two reasons: One, the Ethiopian unoch felt an urgency to be baptized immediately. Second, I am not aware of a conversion in the NT without baptism. You just keep bumping into it. Jesus did it, told us to do it, and his last words were "go, tell, and baptize". Are you saved before or after? That's like debating how many angels can dance on the head of a pin. Only God saves. But the water piece is important. Baptists place a very high importance on it, and CofC places a matter of urgent importance on it. I don't see it as a salvation issue either way - I've never personally met a Baptist follower of Christ who wasn't baptized.
Now, what DOES bother me...there is a non-denominational mega church here that is doing GREAT things. But I got a bulletin last year in the mail as to their youth evangelism. It said something like "We had 82 people saved this year in the youth; 13 baptisms." To me, something isn't getting taught there that is very important. If not even 15 percent think immersion is important, that's kind of messed up. I don't like it at all.
There is a misconception that baptism can only be performed by a minister, etc. Not true. I baptized both my son and my daughter and I am just a regular guy. I, myself, got re-baptized 5 years ago in my neighbor's hot tub. Not because I didn't feel I was saved beforehand, but because I was 15 years old when I was first baptized and I did it only for peer pressure - I did not give my life to Christ and there was no sincere pledge of good conscience. I just wanted to fix that.
OK guys take your shots!