I was lucky that I managed to get all of them for less than $14 each, including the magazines. It's a good start, now I've got my eye on a few more. I'd love to collect them all, but it's not cheap and I'd need to make room since I have a couple other collections that take up some space.
If you're in the US or UK, you can purchase back issues from the online store. For someone like me in Canada, I'm limited to what's available at the local comic/collectible stores or what I'm willing to pay for on eBay, which has gotten a little nuts lately (I paid I think about $60 CAD for an Enterprise-B, which I think works out to about $45 American or 35 pounds).
You mentioned you got an Enterprise-D. I would still recommend getting the 3-pack of the C, D, & E. It's probably the cheapest way of getting the other two. (I got it myself, despite having a D already). If you don't want duplicates, you could always sell one of them.
In terms of some other ships I got that I really like, I think they did a great job with the Defiant. (I've seen some with a pennant facing the wrong way, but mine doesn't have that problem). The NX-01 looks great. So does the Akira class, the Jem'Hadar battle cruiser, the Romulan drone, the 22nd century Klingon Bird-of-Prey (they did an amazing job on the tiny details with those last two), the Breen ship, the New Orleans class, the ECS Fortunate and the USS Centaur. I think the Enterprise 1701 from TOS looks really good too.
In terms of some of the lemons of the set, I've seen pictures of Voyager and I'm not really impressed. I could probably get over the lack of pivoting nacelles, but the font for the registry number is all wrong, and there's a very noticeable seamline around the sides. The two that people rag on the most is the Enterprise-C and the Negh'Var. The "C" is missing some important details but I still like it. I agree that the Negh'Var is a disappointment, however. The Tholian ship also has a very unsightly seamline cutting across its nose. The Steamrunner class isn't a bad model (apart from the deflector dish), but having the stand clip on the back was an unfortunate mistake for a simple reason: With Fed ships, the saucer is pretty much always metal, making them VERY front-heavy. Normally, they have the stand clip on at the saucer, but for whatever reason, they didn't do that with the Steamrunner. Instead, it clips on at the very back and is VERY prone to falling over. (They should've just had the stand come up through the gap behind the saucer, as it does on the NX-01 and Akira).
One thing I'd really like to do is have the actors sign the magazine for ships associated with their characters. Obviously getting one of the regulars to sign the mag for their show's "hero" ship is a no-brainer, but beyond that, you could have Gates McFadden sign the mag for the Pasteur, George Takei sign the Excelsior, Jeffrey Combs sign the Andorian or Jem'Hadar ships, J.G. Hertzler sign one of the Klingon ships or the Saratoga (he was the Vulcan captain, remember?

)
Awww... I have a soft spot in my heart for fugly ships like that. I don't know why. And some of the DS9 FrankenFleet (including that one) really pushed the limits.
Can't say the same, myself. And most of the Wolf 359 ships are even worse, apart from the New Orleans and Cheyenne class. Heck, there's one that's just a saucer and single nacelle. Yuck!