Undoubtedly WD's drive line-up is confusing, and needlessly so IMHO. While I understand the differences between Green, Black, and Raptor, there are other differences still to consider (e.g. the A/V drives). I'll try to break down what I do know and understand.
First off there are 5 major categories: Desktop, Mobile, Enterprise, A/V, and Solid State. Now I find those categories to be a bit stupid as obviously enterprises may need Solid State or A/V-oriented storage for example. I would just have the 3 as it seems sensible to break it down by market segment. But hey, this is what they have. Ignoring the mobile and solid state areas for now as they don't seem relevant to the discussion, we have 3 categories of traditional hard drive storage lines.
Desktop: Basic home-user stuff, covering the range from low-end (budget) to average user to high-end home user (including gamers). This is where the Blue is, along with Green and Black.
Blue is sort of a legacy line of bog-standard drives with no high performance or power savings tech in particular. They're also the only drives to come with traditional PATA connectors anymore, since they're essentially legacy tech, and they also only go up to 1TB. These will probably go away eventually. Here's The Inquirer's take on them "Blue represents the same old line, mainstream drives with nothing to really stand out from the crowd. This is the drive that goes into OEM PCs, or when your family member wants more storage space in their 'CPU' to hold more pictures from 'the intarnets'. Think value." What's interesting is that these are all 7200RPM drives, unlike the Green Drives, however with lower densities per-platter they may be lower performing anyway. 3 year warranties for these.
Green are squarely focused on power (and heat and noise) savings. They have various power saving technologies, but one of the main ways they save power is using lower rotational speeds. This does reduce performance. This is somewhat mitigated by the large(r) sizes of these drives. In fact the Green series are the largest drives they make (the only ones currently with 3TB capacity). They tend to have large caches as well, presumably to offset the performance issues of lower (or variable) rotational speed. 3 year warranties here as well.
Black are the high-performance, full 7200RPM rotational speed drives. Main differences as far as I can tell - besides the rotational speed - are large cache sizes, up to 2TB size (Blue 7200RPM drives only up to 1TB), and, perhaps most uniquely, 5 year warranties. They also claim they have "dual processing" technology, whatever that might mean. Presumably higher performance. It's also likely that they have a higher Mean Time Between Failures (MTBF) rating (which would justify the 5yr warranty), so in other words they're better manufactured and more rigorously tested to tolerances.
Enterprise: Higher-end storage needs, particularly focusing on reliability and performance. This is where the Raptor and RE series drives come in, as well as some 2.5" form factor options. Unfortunately it's also where the naming gets much less clear as - due to it not being end-user oriented - they have done away with the clean, larger brand differentiations (e.g. Blue, Green, Black), and instead have one clear brand (Velociraptor) for just one of their *6* lines; the rest have obscure code names. Most notably all these drives come with 5yr warranties suggesting higher MTBF and manufacturing standards, testing, etc.
The Velociraptor's are easiest to explain. They're maximum performance and consequently smaller storage size. They differentiate from the Black drives in the consumer area by having even higher rotational speeds at 10,000RPM. These are also one of the drive lines in Enterprise that have some models in the 2.5" form factor.
The WD S25 are 2.5" form factor drives running at 10,000RPM for smaller size computing in the enterprise where performance still matters, though it's not clear to me what the difference between these and the 2.5" raptors would be. Not really worth elaborating much more than that in any case.
Here's where it gets "fun". The RE SAS drives seem to possibly contain additional error correction and vibration compensation tech, but it's not clear if those technologies *aren't* in the other enterprise or even desktop drives. They're certainly the focus of the RE SAS drive marketing though. Other than that, the RE SAS is a 7200RPM drive so differentiating from the RE-4GP below, it's going to be faster overall. Doesn't mention dual processors though, which is interesting.
The RE4 series seems to be the sort of "standard high-end" drive with no particular differentiators, just carrying the Enterprise flagship features of 7200RPM speeds and 5yr warranty with higher MTBF, etc. So no dual processors, no green tech, no vibration compensation or extra error correction.
Finally, the RE3 claims to have extra special vibration compensation tech for "high vibration environments". How this is different from the vibration compensation in the RE SAS drives is not clear. It also only goes up to 1TB capacity, which is interesting. 7200RPM drives.
Finally the RE4-GP is basically the RE series but with green tech. Kind of like a desktop Green Drive with dual processors and a 5 year warranty. So faster than the desktop version and more reliable, but still with power-saving tech and not using 7200RPM max performance speeds.
A/V: There are 3 A/V options. To my mind only 1 is worth talking about because the other two only come in sizes up to 500GB. One of them is evidently a legacy drive as it comes in a PATA option, the other is 2.5" form factor. The WD AV-GP is their high capacity media-oriented (a/v = Audio/Video) drive. It's very similar to a desktop Green Drive, using Intellipower, no dual processors, and only has a 3yr warranty despite claims of "enhanced reliability". The main difference seems to be claims of enhanced noise reduction, down to sub-audible levels. Presumably this is all the same tech as other drives, maybe just particularly tuned for low noise environments, or perhaps binned like CPUs based on inherent post-manufacturing noise characteristics.
So yes, you're right that things are confusing, and needlessly so, but that's *mostly* true in the Enterprise area of their market. That is probably not coincidentally also the area where there are more dollars to spend and there is less concern for purchase paralysis from too many choices, and more likelihood of organizations being really picky about their options and maybe even taking advantage of all the different options.
Now all that out of the way, the reality is there's not much need for the average person (or even a techie) to look at the enterprise drives unless you're planning to put together a RAID solution. *If* you're doing that, then it might be worthwhile A: for the reliability and B: because apparently there are some response time differentiators that make them more suitable for working with RAID controllers that expect a fast response. I haven't been able to get real clarity on that latter issue, but there are claims that e.g. Green Drives are not good in RAIDs (though I think my company has at least 1 RAID 5 array running on 2TB green drives doing just fine for the last year or so). I believe the Caviar Black drives are fine in RAIDs anyways, regardless, and it probably has more to do with issues of the Intellipower variable rotational speed system than anything else.
In the end the way I look at it is this: MTBF is a measure of potential reliability as promised by the manufacturer. If the manufacturer believes their own numbers, they will back it up with a warranty. So if I want reliable, I go for the drive with the longest warranty. In this case only the Caviar Black in the consumer space offers a 5yr warranty. It also happens to be the highest performing, and be more expensive than the Blue or Green series. If you want max capacity, the Desktop Green Drive line is the obvious choice as it's the only one with 3TB at present. If you want to construct a RAID, look at Caviar Black or maybe one of the enterprise drives, although on Newegg a lot of the enterprise drives have surprisingly bad reviews and high failure rates. The Caviar Black seems actually more reliably (by ratings/reviews) than the enterprise drives *and* is less expensive per/GB, so that seems to be the best bet for high-end home use.
Hope that helps.