1. http://vietnamvisapro.com - this is my current agency of choice.
2. https://www.myvietnamvisa.com - I use to buy the visa from them from 2007 to 2011.
Note that you can only use this online visa when you arrive by air (Hanoi, Saigon (Ho Chi Minh City), DaNang, Haiphong, Can Tho and Phu Quoc). If you are coming in by land, contact a travel agent in Thailand, Cambodia or Lao for the visa.
1. You fill in the online form and make the payment via their online payment link.
2. Look out for their email that acknowledges your submission and payment. This should arrive within an hour. Check your spam folder. If you don't see the email, just email them back.
3. The agency will send you an email in a day or two with the invitation letter. Usually the first page is a text acknowledging that the persons listed in the following pages have been granted the arrival visa. The following pages have a list of names, including your name. Print all the pages, even the pages that do not have your name. Most agencies will also include a link to an arrival form. You can print and fill this beforehand to save time. This form is also available at their Visa on Arrival counters. You will need to attach a photograph to the arrival form.
This is how the immigration area looks like at Saigon's (Ho Chi Minh City) Than Son Nhat Airport. Walk over to the visa stamping counters. They are marked as A in the illustration above. Submit the passport, invitation letter, filled arrival form, photo and the visa fee. They take about 10 to 20 minutes depending on the volume. You can rest at the waiting area (B). They will then call out your name and return the passport and a receipt for your visa fee payment. Walk over to the immigration counters (C) in the figure. The officer here with make an entry stamp on your passport. You can then go down the escalators (D) to pick up your bags and walk out after a customs inspection.
The procedure is similar at other airports where this facility is available.
Just after the immigration counters there is a currency exchange counter. I have found their rates to be better than the counters elsewhere in the airport. They will also sell you a SIM card. Though it is easy to find WI FI in Vietnam, I would recommend getting a data SIM card - they are inexpensive.