The only hatchable Agumon is the one from Adventure series. (it become WarGreymon, then Omegamon by jogress or VictoryGreymon). You only need to fight Agumon's evolutions until they drop hatchable eggs (shiny ones, with blue background). Here are the locations: Greymon Western Area: East Levels: 20-23 MetalGreymon Ruined Historic Levels: 31-35 HellMetalGreymon Western Area: West Levels: 46-51 WarGreymon Dark Tower Wasteland Levels: 59-62
Then you'll need to collect dragon datas: you get it by scanning dragon type data or magic eggs, dropped by any dragon digimon. You need AT LEAST 15 datas to hatch it at minimal size, but often a injection will fail, so collect more.
At the incubator with the egg and datas: register the agumon hatchable egg, click on "input data". Make at least three successfull inputs and then if you want a minimal size Agumon click on "hatch". Or you can try to get a bigger one by inputing more datas (max:5 successfull injections). Beware: the egg can break itself at each time you try to inject datas.
edit: sorry I was not logged.