I am trying to decied which bike to go with. The is a 2 part answer so please answer oth if you can then give you input. I am trying to find the equivalent to the Trek 5000 In Specialized's line? That is questinon #1 and then of the two which is better dollar for dollar and overall.

Hmm tough one.
I was looking at the 5000 during the "Tour Sale" when they were going for $1800 (at least by me). At the time I was comparing it to the Spec Tarmac Comp (05). The trek had a smoother ride than the Tarmac (I thought) but not a huge difference. I had my mind made up to go that route, but then my LBS reduced their tarmac to $1499. While I was looking at that again, they mentioned a new Allez Comp coming in on sale for 1299 in Team Gerolsteiner livery.
When I rode that I knew it was the bike. It has the goofy 'Zertz' inserts which may do nothing, but it felt about as smooth as the Trek or the Tarmac. The bike just felt 'right' to me. NO Flex (I am about 215lb) just fast and smooth.

Of course YMMV, but I would definately take a look at the Allez's before resigning yourself to go full carbon. I did and saved a few hundred to put towards other goodies.

I had 2005 Roubaix Comp and now have a 2005 Madone 5.9 110-OCLV so I can speak from both sides.

Roubaix had a very nice ride and friendly geometry. Madone is not far off it and is a faster handling bike but for long distance open road ride nothing beats Roubaix carbon for comfort and it gives nothing away in speed to the others, IMO. Madone is not dull unlike what many suggect. But what fits your body better because both are fine bikes. Madone fits well to people with longer upper bodies and shorter legs better or those who like their saddles relatively low, i.e. pedal heels-down style as opposed to toes-down.

I'd be more concerned with how they fit. Trek has a relatively long top tube and Specialized has a relatively short effective top tube. There is also a big difference in the way the nominal sizes are measured between these two brands. If you fit size 5x in a Trek doesn't mean you'll fit size 5x in a Specialized. Depending on your inseam and torso measurements you'll fit one of these two brands much better than the other.

Al

Have you test ridden a Cannondale yet?

How many of you have actually looked at Trek and Spec geometries? Trek being longer than Specialized? Not a chance. Look at a Madone compared to a Tarmac (btw, tube lengths are equal for Tarmac and Roubaix) Trek 56 = 56.1 Tarmac 56 = 56.5. That's effecive top tube on the specialized, of course. Now, since Specialized runs a compact geometry, it better suits those with short legs, like me. I can still have a respectable amount of seatpost, and a normal saddle-to-bar drop while getting the length I need. A trek with a long enough top tube would give me about an inch of seatpost and no drop to the bars. Maybe that works for riders with less flexibility and who want a non-aggressive position, but for a racing setup (which madones and tarmacs are intended for) Trek better suits longer-torsoed peoples.

FWIW, I work at one of the larger dealers for both brands. I size (properly) people to these bikes daily. Trek is a very very average-joe geometry. It's about as standard as you can get, maybe a touch on the short side even. Specialized is a bit longer in the TT, but still pretty much average. Specialized geometry works a lot better for me personally. Think of it this way, when Seven custom built me a frame, I test rode a 56cm Madone to make sure the sizing was right. Now I just ordered a 54cm Tarmac S-works SL. I'm only 5'7 and have a much-longer-than-average torso. My height alone would indicate I might fit best on a 52, but the 54cm Spec is perfect and the Trek is too small.

As for themselves, Specialized gets my motor going more. Their bikes turn me on so to speak. Treks just bore me. Maybe it's because I sell them so often and they're so common, but the aesthetics, paint, and technology is all pretty ho-hum to me. Even an SSLx or a 6.9 (when it comes out) I find bland. Specialized makes their frames look good and I think they're really pushing the envelope in R&D as opposed to Trek which is still selling entirely based on the Lance factor. Build quality-wise, though, they're both impeccable and effectively equal. I've known nothing to separate them.