Is it a better idea to play The Missing Link DLC during Human Revolution or as a standalone game?
Solution 1:
The Missing Link stands apart as an episode by itself, even though the timeline in which is happens is during the main story;
During the main plot of Deus Ex: Human Revolution, there’s a point near the end during which you climb into a pod in order to get to the Panchea complex. When Jensen climbs out of the pod on the after arriving, Pritchard mentions that you've been out of contact for three days.
The Missing Link doesn't affect your main story progress, you can feel free to play around with any Praxis Points you come across and it won't affect any progress on any achievements you've been working on in the main Deus Ex story line as it isn't integrated into the main campaign.
Update (credit to Diziet): Certainly would recommend not playing 'The Missing Link' until the point in the game detailed in the spoiler.
In Deus Ex Human Revolution: Director's Cut, the Missing Link content is built into the main story and does directly effect your main story progress (including Foxiest of the Hounds and Pacifist).
Solution 2:
Missing Link is essentially standalone. Chronologically, it happens in the second half of the main HR story.
- Definitely don't play it before getting to the "missing three days" cutscene in the main story. It won't make sense and there'll be some spoilers.
- I don't really advise playing it chronologically (see below).
- Nothing wrong with playing it after finishing the main story. This is my recommendation.
The reason I say not to slip it into the main story chronologically is just that the flow of the main story gets upset. It's expected to have temporary diversions, sidequests, etc in a longer RPG like Deus Ex, but Missing Link is a fairly big chunk and noticeably isolated in terms of gameplay and social contacts from the rest of the game. Basically, in my opinion it would harm the main story to spend so much time on an off-shoot.
The other nice thing about doing it later is that because you start with a clean slate (in terms of augs and equipment), you don't feel bound to your choices of direction in the main game. That lack of continuity is actually kind of liberating if you tend to play the main story with a strong idea of who your Jensen is.