Deus Ex only had a few moments with slightly difference based on your actions. The first one is the boss' reaction to your first mission depending on how violent you are in your approach. You get a few lines of praise or a chewing out and the weapons master will issue you some different gear for the next mission. That's about it. Later on, there are smaller difference I think like whether to manage to get the code word to activate a kill switch, whether you save a hostage... but the consequences are fairly minimal and confined each time.

I'm more impressed with the handling of consequences in Mass Effect 1 to 3. If you carry a single save game through all three games, the third game can become drastically different. One member of your party won't survive ME1 (it's your choice who that is) and the other one will substitute for them in ME 2 and 3. You can lose an almost arbitrary set of party members at the end of ME2. ME3 has a set of alternate party members to draw on when the main ones are gone. The fates of multiple NPCs can carry through all three games and end in very different ways (e.g. Karin Chakwas, Conrad Werner, Gianna Parasini). The controversy of the ME3 ending aside, the last entry of the series changes remarkably depending on your earlier decisions. Getting all of this straight must have been an enormous effort.