Okay I have been looking at a the topics on the existing nav bar and you are not too far off of what needs to be there.
I just have a "News" section instead of whats new. And I wouldn't bother putting a "submit news" link on the navbar. Just have a submit news link on the top of the news page itself. Afterall, that's going to already be the opening page when you get here (on a side note... please no flash intro screens...) and that's where you are going to be submitting news from anyways.
The Search section... I would personally get rid of this. Instead, at the top of every page, I would have a search field you can simply type into and click search. it's fast and easy. I love Mozilla Firefox because of all the built in searching tools and extensions. I can click in the upper right hand corner search field, choose what search engine I want to search (literally hundreds to choose from) and type in something to search, and click enter and I'm off to the results. No one wants to goto Google.com and then type in your search. I'd rather just do it from wherever I am at. This is the exact same concept I suggest for the BYOAC layout on having a search field at the top of every page.
The Step by Step newbie guide... first of all, I hate that it does this popup window thing that opens over the main page. Freakin browser highjacking I hate it! I was typing stuff in here earlier when I clicked on it and I couldn't come back and lost everything I was typing... augh... stupid javascript. Anyways, this Step by Step guide needs revamped a lot I think. Perhaps pull parts of your book into it. Of course, then you are giving away your book content for free... I dunno if you want to do that.
Controls through Game Consoles look pretty good...
Some of the other topics are sort of unclear. "For Sale" to me tells me it's a message board with people posting stuff for sale... but it's retail stuff... perhaps rename that.
Alternatives needs a different name... i dunno
Tech & Tips - is it just me or is this entire site "Tech and Tips" already? I mean we are building our own arcade machines for goodness sakes.... Every single section looks like a sub category for some Tech and Tips section

Anyways, it looks like a lot of the content in there could be moved into different areas...like controller specific stuff into the controls section. If I am in the controls section, ALL the info regarding controls should be in there. All the 'tech and tips'. All the retail stuff regarding controls. All the reviews of controls. Everything. No one wants to go to 4 or 5 different sections to see all the stuff on controls. People get bored with clicking too much and they want to leave or get frusterated cause they can't find what they want.
Reviews... hmm reviews should be split up into other sections. For example, if I'm in the Controls > Joystick section and I want to see some reviews on specific joysticks, the links for these revews should be right there for me to click on... I don't think I want to goto a different section and start searching for what I want. That hinderance alone sort of makes me not want to bother to look for reviews at all cause it's just a pain. A general rule of thumb for the site is that you shouldn't have to click the mouse more than a few times to get exactly where you want to go. You should haven't search and dig through some huge page to find what you want.
Downloads also good.
Examples is good, but needs revamped. It's a pain in the but trying to wade through 1000 different project names.... there must be a better system for searching easily. I like how you have different systems filling out different things (joysticks, types of buttons, wheels, spinners, arcade vs crt vs tv, etc), but I think you could add a lot of detailed categories into this to make detailed searches easy.
On a quick side note, have you ever thought about what it would be like to actually host peoples project pages on arcadecontrols.com? Instead of linking to external ones I mean? Usually project pages don't consist of too many images and usually just some blogs of how the project is coming along and stuff. You could even offer some hosting options and charge for it. Then people could have some accounts where they get on here and update their page with whatever they want. What would you think of this?
Submit project, in my opinion is a subset of "Examples" so it should be on the examples page.
Msg board (the most clicked on topic on the site I bet), is good, but should probably be quite a bit higher on the list.
Chat room... i see a few people in here every know and then, but is it really helpful?
Links section... it seems to me that all the Links in there could belong in their own respective sections.
Regarding the actual content of each section I just went through, I didn't look deeply into most of the content, but a LOT of it needs to be MAJORLY updated.
saint I like what you said about having subjects of each section. That is a great idea. Do NOT do the 'blog' type pages for the sections. It's impossible to find stuff easily. For example, for the Controls section, don't have one big page with Buttons, Dance Pads, Joysticks, Steering Wheels, etc all on it that you have to scroll through. Each section should have it's own section/page(s) dedicated it alone. I mean, there is a LOT you could say about Dance Pads or Buttons or Joysticks. There are so many different types of joysticks it's not even funny and a lot of information could/should be provided about every single one. You have lots of retail sticks that all the info about all them should be right there, along with links to the retailers sights and review of the joysticks. Then there are all the NOS and discontinued joysticks out there that should be listed on here. Along with reviews and perhaps hints on where to get them used or NOS. This joystick thing is just an example of all the info that could go into a single section and it shows why each subsection needs it's own series of pages dedicated to itself alone.
I think that keeping the menu's on the left side is good. It's the most common way to do it on the internet. I wouldn't be to into the topics/sections listed on the top... there is just too much info here for that.
Static menu choices are good. But if you are in a section with subsections, those subsections should be integrated into the navbar accordingly.
Staggered menu choices are good. It will keep things organized and help people get to what they want more easily.
Okay thats all I can think of for now. Hopefully this will help you saint.