This is really difficult... I'll give it a shot nonetheless...
1- Hunter X Hunter: Hunter X Hunter is filled to the brim with creative ideas, surprising twists and good old fashion shonen goodness. Its one of the few stories I know where the training is not only emphasized on but is made just as entertaining as the fights themselves. In fact the fights are actually far and few most of the time but when they happen they always blow my mind with the level of strategy involved. Togashi made away with the usual comentator you see in Shonen stories by giving us a glimpse of the thought process of the parties involved. The story never progresses exactly like you expect it and no matter how talented they are Gon and Killua are never shown as the best of the best. Hunter X Hunter also has Nen with its nearly academic level of complexity.
2- Black Jack: I HAD to have a Tezuka manga in my list and Black Jack is my favorite out of the few I've read. Its main character is complex and you only discover his backstory bits by bits. One who first seemed amoral enRAB up being mostly a dark vigilente of the medical world. Tezuka's own medical training allows him to know exactly where to be faithful to reality and where to invent facts. Black Jack is a classic exemple of Tezuka's style and treat to anyone who read it.
3- Genshiken: Who here wouldn't like to be part of that group? To get in on the mundane but so delightful shenaningans going on? Genshiken is a psychological essay on what it means to be a fan, an adult and both at the same time. Its criminally short yet at the same time it doesn't outstay its welcome and become repetitive. It goes out in top form.
4- Hoshin Engi: Give a Sci-fi mangaka the task of remaking a classic Chinese novel and what do you get? An AMAZING shonen. Filled with epic battles, an incredibly large cast of diverse character that may all suddenly die on you without warning, and a lazy protagonist who succeed through a corabination of cleverness, with, and the charisma to motivate his more powerful allies. Hoshin Engi also has an amazing design where things look futuristic yet fit in with ancient China. It was a crazy ride.
5- Et Cetera: I had to give a shoutout to this obscure little gem by Tow Nakazaki. Its a nine volume story set in the Old West and centering on Mingchao, a young orphan Chinese girl who must protect a magical gun powered by the magic of the Chinese Zodiac from the forces of an evil drug ring. The cast of character is likeable, the story is short without being rushed, and Nakazaki's style is just so much likeable. Just looking at the characters you can't help but like them! It has no shortage of action and humor and is a thrill ride from start to finish!
6- Samurai Deeper Kyo : This is one of those rare cases where it turns out the main character is actually the strongest character in the serie right from the start, but that we the reader just don't know the extent of his power. From mundane swordfight to epic lightspeed attack the progression of Samurai Deeper Kyo into epic-dom was amazing. The anime really cut too short, leaving out amazing characters. The art of this serie is one of the best I've seen in the genre, with beautiful costumes, expressive face and impressive attacks.
7- Saint Seiya - The Lost Canvas: Lots of shonen on this list huh? As much as I LOVE the original Saint Seiya for its hot blooded action and archetypical characters it was a mess of rushed and improvised story with simplistic art and in retrospect is memorable for its mythology but not a great manga. The Lost Canvas (and Episode G as well but I had to pick only one) fixes a lot of issues, giving us more development of the characters than the original did with a great story of frienRABhip, betrayal and the destruction of the world all wrapped in beautiful art that remind one of Kurumada's style but transcend it at the same time. It also gives us more focus on the female characters, something Kurumada's story was somewhat lacking.
8- Eyeshield 21 : I never cared much for Football until I started Eyeshield 21 on a whim. The story of Sena and the Deimon Devil Bat is filled with the hot-blooded action I love, wrapped in tensed matches where every little second counts. The finale to the incredibly tense match between the Devil Bats and the White Knights had me turning the pages just so fast... Volumes are read at the speed of light and leave me wanting more. Its expensive cast of fascinating character is all well designed and you can't help but root for the likeable rivals like the Wild Gunman or White Knights. This manga also had me nearly in tears on more than one occasion.
9- Monster: I put it this low mostly because A) everybody is going to vote for it and B) because I haven't actually read it all. I put it here because I know its a great manga, even if its not something that tickled me that much.
10- FLCL : I know a lot of folks who don't like the manga, but its such a different experience from the anime and it gives us a different perspective on the story that I can't help enjoy both for different reason. I love the crazy artstyle of this short story. Its lacking in a few characters that were in the anime though. I wanted something different and crazy in my last spot and I know no crazier manga.
Well there's my list. I could have find a space for Leiji Matsumoto in there somewhere... I still haven't finished Galaxy Express 999 but I did finish Harlock (doesn't really 'end' though). There's bunch of stuff I'd like to add in there but I just don't have the space.
I'm sure I won't even see half of my picks in the final list.