07-Ghost (99+) - Complete. Technically it's 1 chapter short of being 100+, but I'd still consider it. If you include 07-Ghost Children, you get an extra 7 chapters.

Übel Blatt (135) - Ongoing.

Trigun / Trigun Maximum - Complete. Chapter numbering is a bit odd here but it does work out to a little over 100 chapters if you lump them together as one series.

Gunnm Last Order (124) - Complete. However it's prequel Gunnm should be read first even though it is only 52 chapters. The third series only recently started thus is only up to chapter 8.

Angel Sanctuary (120) - Complete.

X (104) - Permanent Hiatus / Discontinued

Chi's Sweet Home (164) - Complete. Only 103 of these chapters have been scanlated.

Tsubasa - Reservoir Chronicle (210) - Complete.

Karneval (87) - Ongoing. It's probably going to hit 100+ before it's concluded.

Amatsuki (100+) - I'm pretty sure that this one has hit 100+ even though only 87 are scanlated. Just a warning though on this one, it is one of those series that keeps going off on convoluted tangents... recommend waiting for the series to finish before reading.

If you also consider the number of volumes, there are other series that technically could fall under the category of being long despite not having nearly as many chapters.

Completed Series:

Chronicles of the Cursed Sword - 37 Volumes (not sure if fully scanlated)
Konjiki no Gash!! - 323 chapters
Bamboo Blade - 102 chapters
Battle Royale - 115 chapters
Fruits Basket - 136 chapters
Hanazakari no Kimitachi e - 144 chapters
Inuyasha - 557 chapters
Majin Tantei Nougami Neuro - 198 chapters
MAR - 159 chapters (+36 chapters for the sequel)
Ranma 1/2 - 229 chapters
Rave Master - 296 chapters
School Rumble - 283 chapters (+10 chapters for sequel)
Tsuki no Shippo - 105 chapters
xxxHolic - 213 chapters

Kubera
Tower of God
The GOD of High School
Wake Up Deadman
The One