Allow me to contribute my US $.02.
I've followed PCgen for quite a long time. It has gone through many changes, and my opinion of it has changed with it.
To wit: prior to a couple of months ago, I found PCgen ugly, highly unituitive, slow and bug-ridden.
Today, I find PCgen less ugly, mildly unintuitive and well, slow.
Now, this may sound like a negative review. It is not. Allow me to go into greater detail.
First off, PCgen's flexibility and scope are impressive, and always have been. The widespread support that PCgen now enjoys amidst d20 publishers is both impressive and heartening. Many features have been added that make it a very valuable tool for me, as a DM. Some of my players have adopted it for their own use, based on my announcing that I was using it.
What does PCgen do well? Character creation has finally become easier to do with PCgen than with a custom Excel spreadsheet. While it's GUI is still cluttered and somewhat counter-intuitive, it's better than it was, and shows signs of continual improvement. PCgen is a very powerful application that truly allows you to design very odd combinations of characters, allowing a DM to override all the basic options to create an 'illegal' character, rules-wise, and create custom items.
What does PCgen do poorly? Many options are poorly or not documented at all. For example, many options require terminating the program and restarting it for changes to take effect. This is mentioned nowhere in the program, and a simple pop-up could save an hour's frustration. Many options don't work in the same way as similar features, and the only way to discover this is by trial-and-error. Most likely as the result of so many different team members, there is no GUI design standard, and this leads to a confusing interface. Creating a new magic weapon was almost enough to cause me to delete the program, when I attempted to create a +2 halberd for a character. I eventually sussed it out (it involved shutting down the program and restarting), but it should have been much easier than it was. Other problems are ones that will continue, thanks to WOTC's strict enforcement of the OGL...specifically that many incomplete LST files will never be completed, except perhaps as black market materials. This will hopefully change...but given it's been almost three years, and nearly half of the three core rulebooks remains unreleased to the SRD officially, this remains dubious. I really had wanted the Axiomatic template from Manual of the Planes, for example.
And let's be clear....it's SLOW. I mean, SLLLOOOOOWWW. Java 1.4 changes this not one jot. Is it faster than it once was? Perhaps. But it's still mind-numbingly slow in spots. It's an acceptable situation, but I sure hope that there are a lot of Mac and Linux users taking advantage of this program to make it worth the performance cost. A major disadvantage, given that I like to run things on my laptop, and I CAN run eTools, but PCgen is far, far too slow to be usable there.
The worst thing about PCgen? It's FAQ, or the lack thereof. Perhaps this has changed, but when I went to sourceforge and followed the link to the FAQ (after having spent a half-hour knocking my head against a wall), and then read a irritating message that mockingly declared that PCgen didn't need a FAQ...well, if I'd found the author of said message, I would have taken him behind the woodshed for a beating. Maybe someone thought it was cute, but it was bad form, at best. The people most likely to need a FAQ or the folks most likely to not want to read such tripe.
How does PCgen stack against it's competition? Well, I consider it to have two major competitors: Homebrew Excel sheets and eTools. LonePaladin's sheet is a very popular one amongst my players, and before he stopped updating it, was our campaign standard. It has a clean, intuitive interface, using clever advantage of color and design, good printing options, and it worked really well for the core materials. In many ways, I still consider it superior to PCgen. What it lacks, though, are options. It is unsupported, and doesn't cover anything outside the core rulebooks. It doesn't have a lot of flexibility, which is badly needed at 16th level, far more than at 6th.
And what of the dreaded eTools, once consider to be the frontrunner of the chargen apps, that would lay waste to all in it's path? Well, it's OK. Given the proliferation of DBAs and amateur Access programmers, it's as easily modified as PCgen is, perhaps easier. It has a cleaner interface...but it isn't always as intuitive as you'd expect it to be. Granted, the chargen program that came with the PHB was much spiffier, but I was expecting them to build on that, not just cobble together a bunch of screens from FoxPro. One place eTools really disappoints is in performance...it's just not as much of a speed improvement over PCgen as I expected. Some parts of eTools are fantastic, and others are very weak. This was Fluid/WOTC's category to win, and they appear to have 'phoned it in', so to speak. The lack of things such as templates, and poor support so far are baffling and irritating. In general, I consider it a worthy rival to PCgen, neither conquered nor conqueror.
Ultimately, I think that PCgen is a worthy DM prep tool, and an excellent chargen tool. I still have my LST files since before Gencon, so it's worth using, for me. Without that functionality, eTools would probably win out slightly, but with better support and features supported that eTools apparently forgot about, PCgen isn't getting deleted off my machine anytime soon.
Hope that helps.