1. Monster- Normally I'd rank Death Note or Rurouni Kenshin as my favorite manga, but this series definitely deserves MUCH more love than it gets.
2. Dragonball- People can say what they want about its various anime adaptations, and in many cases, they are right about its flaws. However, I don't give a crap what anyone says about Dragonball when it comes to the manga. All I know is that to me, this is shounen manga at its peak, and I still have yet to see another battle-oriented shounen manga that's not Rurouni Kenshin or Yu Yu Hakusho top it for me.
3. Rurouni Kenshin- Normally this would be higher, but I moved it down to give the 2 other series above some extra points. That said, this is easily the best battle-oriented shounen manga that I have ever read, period. I know that many people would rather rank series like Naruto or One Piece higher, but this is my personal favorite when it comes to shounen, as I findi to be the most interesting that I have ever read. Also, it gets bonus points for actually having action scenes that are well-drawn out enough for me to actually follow, unlike 90% of all of the otehr battle-oriented shounen manga from WSJ.
4. Death Note- This would also normally be higher on my list, but anyways, the bottom line is that I have always been captivated by this series. I love its concept, story, characters, and its artwork. I even liked the second arc despite the fact that so many others hate it. Oh well, for me, its simply interesting from beginning to end, and that's why I love it.
5. Great Teacher Onizuka- While it does go somewhat downhill with its final arc, the rest of the series is pure fun, and it has some truly touching as well as inspiring moments. I really which that the anime could have finished animating the rest of this (but, then again, there's at least a dozen other manga that I would wish that for, as well ).
6. Battle Royale- Sure, its overly-gory and the artwork can be disturbing, but I feel that this manga is pretty underrated. Its not nearly as good as the novel which its based off of, but its still a great adaptation of it, nonetheless (IMO), and it always managed to keep me on the edge of my seat as I was reading it, despite the fact that I already knew most of what was going to happen since I had read the novel first (it still managed to surprise me and occasionally fake me out with some of its twists whenever it made changes to what had originally happened in the novel).
7. Hikaru no Go- Its a very standard shounen series in many ways, but its also a very addicting one. However, the fact that it makes such an interesting story out of such an ancient (literally) board-game is quite outstanding in and of itself. Also, furthermore, it actually got me into playing the game of Go, and while I definitely suck at it, I have to give this manga extra props for actaully getting me into a game that I would have payed no mind to and just passed off as a boring game which only super-geniuses could be able to play. I'm glad that I did get into it, because it really is a simple yet very complex and fun game that really forces you to heavily strategize.
8. Hunter X Hunter- This is Togashi's 2nd "major" manga series, and it really proves how talented and creative this guy is with his writing. He constantly comes up with unique/original, inventive, and unpredictable ideas, and while the story starts out slow, I have been loving almost every minute of it ever since the later-half of the Hunter Exams arc. Although, having said that, I ranked this manga a little bit lower than where I used to rank it, since after re-reading certain bits of it, I have noticed how it can slip in quality quite a bit from time to time, and that really does hurt its overall entertainment for me, a little bit. But, still, the full package is probably one of the best currently-running (well if you can call a series that constantly goes on 1 year + long hiatuses "currently running) shounen series out there.
9. History's Strongest Disciple Kenichi- Alright, I'll admit, this is a guilty pleasure of mine. It has a ton of shounen cliches, uses the same plot-points quite a lot, and it also has Ecchi (which I hate). However, I just cannot deny that I still find its better aspects to be really interesting, and overall, the story really addicted me. I want to point out now that I don't read that many manga, so its not like this manga had that much competition when I put it on my top 10 list, but I should also defend myself for putting it on my list and say that to its credit, it does quite a few things right. I really do enjoy its sense of humor, characters like Nijima and Siegfried are actually pretty unique and also funny, and I like how despite its insanely over-the-top nature (which is something that's obviously done on purpose, later on in the manga's story line), quite a lot of the corabat in this series is at least "based" off of real martial arts (its exaggerated like hell, of course, though ).
10. Gantz- Its not very consistent in quality, IMO, but when things get heated up, it can be a really awesome series. That's really all there is for me to say about a series like this. I will also say, though, that it deserves credit for actually going so far as to develop a really pathetic and unlikeable main character into a really honest, likeable, and fairly bad-ass protagonist. I can't think of any other series that has has character development good enough to turn around a character's personality that much.
Honorable Mentions:
Yu Yu Hakusho- I do love the manga, but its anime adaptation is even better, IMO, and since it already ranked so high on the top 25 anime list, I decided to leave it out of my list this time to make room for another series. It is still one of my favorite manga, though (normally it'd be tied with GTO for me).
Shounan Jun'ai Gumi!- I'd rank it pretty high on my list if I actually got to read more of it, but unfortunately I have only ever read the first 80 chapters of it.
Fullmetal Alchemist- This is a great manga, and its the version of FMA that I got into first (which is a big reason for why I prefer it over the 1st anime serie adaptation of it, personally), but overall it just barely got edged out of my list simply because I don't find it to be quite as entertaining as the other series that I listed (in that it can often become less interesting every now and then before picking up its pacing again with the story, IMO).
Hellsing- Its more of a guilty pleasure than anything else, though.
Black Lagoon- Once again, another seris that I still need to read more of, as far as the manga goes.
Bakuman- There still isn't enough of the series out for me to actually rank it as one of my favorites, as much as I love what I have read of it.
One Piece- I would have ranked it on my list, but I only started reading the manga after I finished watching the Thriller Bark arc in the anime, so I really haven't actually read that much of the manga (at least not enough to rank it as one of my favorites).