By default, missile teams are armed with the FGM-148 Javelin missile launcher (rev. 4.156). If a scenario designer wants to change that, right-click on the team in question, navigate to its "optional weapon type" submenu and select a different missile type. Note that the way this was done before SB 2.6x (specifying the weapon type by selecting a different missile type in the unit's ammunition window) is no longer functional, as the ammunition window will only list ammo types suitable for the selected launcher.
Note that at present all missiles save the "RBS70 SAM" are anti-vehicle missiles. Additionally, the 3d model of some missiles may be a placeholder and may not correspond to the actually equipped weapon.
Beginning with version 4.000, ATGM teams may use any dismounted movement type available, but fatigue much quicker when jogging or sprinting compared to regular infantry units.
Currently, there is documentation for the following missiles available:
Further information on ATGM tactics and use can be found in the appropriately named guide: How to fight tanks with ATGM by user Kingtiger, and an excellent tutorial scenario covering various ATGM systems by users Toyguy and Gibsonm may be found in the download section here.