There has been a lot of discussion on this board as to travel agents, with some some viewing them as white knights and others as crooks. But there isn't a lot of specific information that would allow you to judge for yourself based on your own needs, so I thought I'd give specifics from my own experience that might be useful. This is based upon having a fairly tight schedule for 4 of us, about 17 days on the ground, stopping in HMC, Hoi An, Hue, Sapa and Hanoi, staying at better hotels, using board favorite Tonkin. There seems to be no question that if you have enough time to change arrangements without impinging on your trip and plan on staying at cheaper hotels, doing it yourself makes more sense than paying an agent. That said, here's our experience.
Hotels: There are numerous sites against which you can compare the price the agent is giving you against what you could get on your own. Tonkin's aggregate cost for the hotels they booked was only slightly higher than if I had booked each separately with the cheapest agent for that hotel. If it had been any more I would have gone with the cheapest rather than convenience.
Sending credit card info to reputable agents does not seem to be a problem. I did so for a hotel booked by Vietnam Stay and last year for hotels in Thailand and Cambodia without a problem. I just made sure that other travelers vouched for the agents on the appropriate forums.
Air: We flew HMC -Danang and Hue-Hanoi. The face value of the ticket was 1,804,000 Dong, about $112. Tonkin charged $140, a $28 commission, for a total of $112 for the 4 tickets. Frankly, I think this is high for 4 tickets, which barely take more effort to write than 1. On the other hand, we had specific flights that we wanted to take to maximize our time, and might not have gotten those flights if we had waited until we arrived. For $112 I think I'd take the risk next time.
Train to Sapa: Tonkin charged us $60 a round trip for the King Express. It was nothing special in the way of service or accommodations. We were not told that this service arrived back in Hanoi officially at 5am, and actually at 4:30 am, until just before we left for Vietnam. We were not happy with this. These trains can be booked cheaper in VN-however, they are often sold out days or weeks in advance. You have to balance the commission cost against certainty if you don't have the ability to radically change your plans.
Transfers and tours: Except for 2 transfers, Lao Cai-Sapa and Hanoi airport, we made our own arrangements on the ground. These transfers cost about $10 apiece more than than the locally arranged returns. We booked tours on our own at rates substantially lower than offered by agents.
Service: Just because you have an agent handling details doesn't mean you shouldn't be vigilant. The first set of hotel vouchers from Tonkin had the wrong dates. I immediately emailed them and got corrected vouchers within a few hours. I don't know if it would have mattered in VN, but I didn't want to give any hotel an excuse for denying our booking.
Vietnam Stay failed to reserve the first day of our 3 day stay at the Victoria, Hoi An. When we arrived, they were full. The voucher had the correct dates. When informed, VN Stay immediately made a reservation at Palm Gardens, an equivalent hotel. While inconvenient, at least we had a place for the night.
On the other hand, when our first choice hotel in Hanoi turned out to be full, Tonkin recommended Hanoi Elegance 2, which, while not very plush, was a lot cheaper and much better located. With the nicest staff and free internet in the room, this was a good steer from Tonkin that I probably would have missed.
To sum up: With the airfare and train commissions and the slightly higher hotel costs, using Tonkin probably cost us less than $200 more than booking everything on our own. With no assurance that we would have gotten our preferred flights if booked when we arrived, I figure it was probably worth it for our first trip. On the other hand, I'm not sure I would have felt that way if we had booked all our transfers and tours, which cost substantially more than easily arranged local alternatives.
I hope this isn't too long and is useful.