Don't be afraid to use the musical cues, a chime will let you know when you have found all the clues in an area. Doing this I got 222 clues just playing the story without using a guide.
If you, like me, have not got the achievement after completing the game, select 'cases' from the main menu. If you replay a case you will start that case with 5 intuition points. Each time you go to a new area to investigate, press 'LB' then select 'show all clues' this will display a magnifying glass icon over every clue in the current scene on the minimap, however, be careful not to leave the scene before finding them all, otherwise the icons disappear from the map.
Do this for your worst rated cases and you should get there quick enough.
The achievement while pop when you search for the clue, there is no need to reach a save, or end the case.
To clear up any possible confusion, the game seems to track total clues in a hidden statistic, while the stat tracker in game, and on the social club seem to track your last save. The game creates a new save for a replay, so this is what is listed on your stat tracker, only new clues will be added to your tally.
There seems to be a few people having issues with this popping well beyond the 95% barrier, which seems to be around 228.
*edit* This is most likely caused by the DLC cases 'Naked City' and 'A Slip Of The Tongue' my assumption would be that these cases do not count towards the achievement
*edit*The DLC cases will give an increase to your stat tracker in game, but don't seem to count towards the 95% of clues that you need.
(Thanks to LitaOsiris)
*edit*All items listed as 'clue' count, not just physical things, but 'possible motive' etc. so to find certain clues, you will also need to branch certain dialogues correctly.
(Thanks to Alita360)
If you are still struggling, using the guide here http://lanoire.wikia.com/wiki/Cases
The wiki will give you a detailed walk through on how to 5 star the cases, Newspapers do not count towards clues, and most other clues are listed on the wiki.