Edmunds is pretty good at getting invoice pricing both on the base vehicle and on the options that may be installed. They don't necessarily have updated information on preferred option packages and manufacturer's rebates.
No question the most important thing before talking a deal seriously is to arm yourself with the invoice pricing AND know exactly what your looking for when it comes time to sit down at the table. Want to know if you got a great deal? Take that invoice price, subtract the destination charge, dealer fees and dealer hold back (all available online). If you got what your looking for at that price or less you did good. If you paid anything over that... well you paid more than you needed to. Now you may say how is it possible to get a vehicle for less than invoice and subtracting all the fees. Oh it is, see the invoice price now a days is still loaded with some dealer incentives that are hidden, and don't forget the dealers make money on volume not necessarily on each unit sold. So the key is to hit the big dealer and press them hard, don't worry they won't make a deal and "loose money" at the same time. If you're really good don't hesitate to negotiate on things they just as soon not even discuss, like for example the kick back they get if you happen to finance the vehicle through the manufacturer. I negotiated an extra $500 bucks out of the dealer by instead of paying cash, financing it - with no pre-payment clause of course which I promptly paid off the first month. Yes it can be done. You'll have to hold your ground and even do like I did and get up and leave since the deal wasn't coming in close enough between what I wanted to pay and what they wanted to sell for. When I left the table we were 3K apart on the price when I came back to buy after a couple of phone calls from the sales manager they came down $2500 I went up $500, in the end I got my new 2011 Toyota Tacoma 4X4 for $1900 UNDER invoice with no dealer fees, prep or destination charge paid. I did have to pay the documentation, but that to me is a fair charge to pay. Oh the sales manager cried he was loosing money - yeah whatever they made money and I told him so much or that deal never would have happened. On the flip side I can tell you right now there is no way right now to get say a Prius for anything under invoice.
Remember hold their feet to the fire, the salesman is NOT your friend or doing you any favors, they have a vested interest in getting you to buy at the highest possible price. IF you have a person that's nice and pleasant to work with - great but they are still not your buddy. Dealer or manufacturer extended warranties are nothing but gravy money for the dealers and should be avoided, if you're buying a quality vehicle you don't need it anyways. Never get suckered into any dealer installed options. Finally there is no free lunch with these guys, like service your vehicle here and get "free" (whatever). Nah they aren't doing that as a favor, they are making money by fooling the customer into thinking they are getting something for nothing and up selling service every time you come in. Those big facilities and fancy show rooms on prime real estate exist for a reason - uninformed buyers getting screwed to various degrees.
Oh and here's my favorite. Don't hesitate to take all that great information off the web, print it out and bring it with you. Reference it often and un-apologetically. If you don't hear what you want out of one dealer go elsewhere. Even if one dealer has what you want, make a deal for that vehicle at another dealer, they sometimes can cherry pick inventory from each other. Better yet negotiate a deal at one and take it in writing to another and get them to beat it (if they can).
If you're buying used that's tougher because "book value" is merely a guide not gospel. There are so many variables in play but the bottom line there is to look around and get a feel for the current market, again only possible after you hone in on exactly what you want. Some things demand higher prices than others just they way it is. Market research will help with that. Condition and a flawless maintenance history trumps mileage. Car fax is your friend never buy without seeing one. Never buy used without having somebody that knows what they are doing give it a once over that is a neutral party. A trained eye can catch most things. Few dirty secrets with used cars.
Certified Used means only one thing. The vehicle visually looks acceptable and falls within a certain year and mileage window. Nothing more nothing less. Don't think the dealer spent hours of time nit picking the car - trust me they didn't, or ever will. Certified vehicles usually do carry some incentives like a small warranty and at times special financing deals.
Plain on used... on a big dealer lot normally these are cars and trucks that are less than 90K on the ticker, less than 8 years old and are in good enough shape where there is nothing seriously wrong with them and have good curb appeal and can be flipped for minimal or no investment. On a rare occasion you'll see higher mileage cars, those are the exceptional few but the problem is they are very hard to get financing for due to the age or mileage. There is a market for those, up until my last purchase that's always been my sweet spot, 6-8 years old with 100K on the ODO. Not for everyone but if you know what your looking at and what to look for in regards to common problems. Hey I've been known to carry my portable ODBII computer scanner with me and pull codes out of the ECU right in front of the sales man

what are they going to say - no?
Small car dealers - 90% of the time is a miss. Why? Their inventory is mostly supplied by big dealer cast offs, as I said earlier the dealers only cast off stuff for a reason and usually a good one. I don't waste my time at small dealers. I'm way to particular as to what I'm looking for.
Now all that said... if you want to know where I bought my new truck PM me and I'll let you know, don't think it appropriate to advertise anyone in this kind of forum. Would I recommend them? Getting the deal I did took time, research and effort, but in the end they were pretty darn aggressive in their pricing but had to be
pushed to get there. That wasn't a strippo model either, it was fully decked out. I think I was treated fair, they didn't try to play any games but again I stood my ground and was prepared to and did walk away.
Finally any good deal you may get will be ruined if you trade in something. You can always beat what a dealer will give you in trade selling privately.