Depends what the aluminium is being joined to. My preferences are Duralac for aluminium to aluminium/stainless steel joints (and can also be used on aluminium to wood). The same for any pop-rivet joints involving aluminium.
Some complain that Duralac sets hard after a while, something which has never bothered me personally, but there is an alternative chromate paste available whic is supposed to not set hard called JC5A (see http://www.lasaero.com/site/products/section?id=CH). Eye-watering price. Both JC5A and Duralac are extensively used for light aircraft fabrication work.
For aluminium to grp, eg window surrounds or toe rails, a non-setting mastic like Arbomast BR (which is what Houdini Marine recommend).