I have only published through the PrePrints section before but I've found it really useful for publishing protocols for reviews and gaining initial feedback, as there are few alternatives in my discipline. The overall experience was very straightforward and quick, the latter most likely due to there being no peer review for PrePrints.

I keep checking you guys out Pete Binfield :D trying to decide whether I will submit my next paper to PeerJ.  I keep vacillating on my decision. As a tenure track assistant prof with funding, ahem, "challenges", I might just take the dive and submit. I was just looking at the author surveys, and they are compelling. I've been asking some of the tenured profs their opinion, many hadn't heard about you, but they seemed positive. I am getting so disgusted by the color charges of the traditional print journals. In my current paper, I have 9 color figures to submit, I have to accept that they are going to be both behind a paywall (unless I can come up with 2-3k) and that I won't be able to pay for the printed version to be in color. With 9 color figures, and an average $400 per color plate, that would be an additional $3,600 in order for the paper version to be in color, although they do allow for color online for free. I feel like it's extortion, especially for young profs who are trying to get their work out, so they land grants and get tenure. To fully get your paper out in those journals and be visible would be 5-6k. So, tell me how PLOS One ($1495) and PeerJ ($300 per author, or $695 flat rate), or even Frontiers (about $2K, although I do get a 15% discount since I have reviewed papers for them lately) are the more expensive models? Especially when I have a companion paper that is almost ready to submit too? I'd love to get your opinion Alan. Did you end up submitting to PeerJ, where you happy with it?

Things that I find unique about PeerJ are - 

1. Their staff are polite and super quick. They reply your query within a day. If they don't reply you can write directly to Peter Binfield - he will make sure everything is smooth from there onward. In traditional journals, you don't have privilege to write a  mail to the director of the company. Staff working with traditional journals are usually rude - they don't answer your queries for ages. You send a mail today - you will get a cold reply only after a week or two.   

2. PeerJ's submission is system is far far more advanced than traditional journals. Its hassle free and modern.  

3. Their APCs are lower than most OA journals. 

4. You can submit your paper in whatever referencing style you like. PeerJ staff will take care of it - they say what you need to do is science, not editing and referencing. 

5. Their review process is quick. They give only 3 days to the reviewer to accept the invitation - if you don't accept their request to review the article they would send a remainder after three days. If you still don't respond they start finding a new reviewer.

6.  Their publication team is awesome (and they are real people with a face and name - you can google them unlike traditional journals where staff has fake names with no picture) - and responds quickly unlike traditional journals where they are mostly lazy and work at snail's pace. 

7. Traditional journal don't care and respect for your time - that is I think is main reason why people are shifting to journals like PeerJ where staff is super quick and do their duty diligently.

8. I remember one of my paper took 2 years to publish  because of slow peer-review -  6 months for the first review - 7 months for the second review.  While in PeerJ, I submitted my paper in January, the reviews appeared in March and by May, my paper was out. 

9. I paid only $299 once and I can submit unlimited number of paper in PeerJ - its not possible anywhere else. 

10. They don't charge even a penny for colourful figures. 

Thanks for your thoughts.

I didn't submit to PeerJ in the end, I opted for a more conventional OA journal (Frontiers in Physiology). My main concern is that it is quite general and therefore doesn't tend to have a specific target readership, although with the internet now, it really is a case of simply getting work out there that is accessible for people to read. I have heard excellent reports about PeerJ and what has been written here tends to support that. I'm certainly going to consider submission for appropriate future papers.

OK, I went through the process and our article has been accepted. I did have some glitches with file size limitation and frustrations in uploading a PDF file, but the staff was very helpful. Their prices have gone up, but I still think it's a bargain compared to others.

They were fast in their responses, in the review process, and proof process.