I've read pretty much every Pokemon manga there is out there. Nippon Export is a God-send. It'd be much easier to list the ones I HAVEN'T read. I haven't read the movie adaption mangas, Snatcher Reo (would if I could, but those who own it are too freaking stingy to share it, despite the fact that it's out of print and thus impossible to obtain), all other Colosseum- or XD-related mangas (I don't know how many exist, since those didn't get much publicity), and all Ranger-related mangas, including Hidenori's version. I don't really have an interest for Web-comics, and I can't find any Ranger mangas in volume-form (although I've heard they exist). I also haven't read those Pikachu-meets-the-press comics.
Aside from that, though... Yeah, I've read pretty much every manga, thanks to Nippon-Export (which is an eBay-like site, Mods, NOT a read-manga-online one, so I doubt plugging it is against the forum rules). I'd recommend Magical Pokemon Journey (PiPiPi Adventures in Japanese). It's a shoujo-manga, which is really weird considering it's based on a shounen-genre; it actually manages to do the job. It focuses a lot on romance and character-development, which I feel PokeSpecial lacks somewhat. It doesn't have much of a plot, though shoujo-mangas rarely do.
I'd also recommend Pokemon Pocket Monsters and its variants/sequels (Pokemon R-S, Pokemon D-P, and Pokemon HG-SS), but only if you value laughs more than plot and character development. PPM is full of laughs and is very charming at times, very disturbing at others (but in a good way). It's even less story-focused than the anime, though, so if you value story in your mangas, I'd pass this one over. Personally, though, I like it a lot.
Lastly, Pokemon DPA and the Electric Tale of Pikachu are okay, though the latter is somewhat overrated, IMO. It's basically an abridged version of the anime with an Ash that doesn't suck at Pokemon and who actually learns from his mistakes and is a decent trainer. I'm not big on abridged things, though. It doesn't mean you shouldn't give it a try, of course. As for DPA... Well, I like it because it's a long manga, and it has story. Although, I don't think it's done nearly as well as PokeSpecial (sorry, I know you're probably sick of hearing about that manga by now XD). But it's still worth reading at least once.