There's not much of particular help to give for this (due to how many various missions there are), but here's some advice and info in general to help.
1) Collect all missions ASAP.
Whenever you enter an area, look around the map for any [!] signs, these are missions for you to receive. Go and get them right away. No missions are permanently missable and they can be completed at any time in any order. However, some side missions won't be available until after other related side missions are done first. As far as when to complete them, that's all up to you. The sooner you do them, the sooner you get the Exp. and rewards, however waiting until you have cleared the game/reached max level (whatever it is at the time) will give you the chance to get the reward items with late/end-game stats, so there is that bonus (though you can always just do that in TVHM or with a new character as well.
Note: There are a few side missions that will become temporarily locked (can not receive, progress, or turn in) during certain main story missions, as key characters will be involved in those missions. They will become available again after you have finished the associated main story missions.
2) Don't miss the six Trials and three Slaughter arenas.
There are six Trial missions that become available after you get an item that lets you read the Eridian Markings throughout the worlds you visit. They are found at various places you have been to, but once you reach that point in the game they will have the [!] marker for you to find them.
There are three Slaughter arenas; two are side zones, one on Pandora and the other on Promethea, and the other is given as a mission on Nekrotafeyo that unlocks a space station to travel to on Sanctuary to reach the Slaughter arena. The planet-based ones can be easy to miss, since their travel spots don't really stand out and aren't required to visit for any story missions.
Note: These nine missions have the special feature of always matching your level, so it may be best to wait until you either have a good partner(s) as well as end-game gear.
3) This achievement notably does NOT include any of the Bounty Board missions for hunting rare-spawn enemies (found on the wall between the players' rooms and Moxxi's Bar), so don't worry about those. (Definitely grab those missions if you see them though! Those rare spawns can be annoying to find!)
4) For those new to Borderlands, no DLC missions are included as a requirement for this. This includes not just paid DLC but also free DLC (such as the Takedown missions). You only need to worry about the missions that were part of the base game at launch.