One thing skaw didn't mention is that with each upgrade, the cost in terms of the amount of merits increases. So if you want to upgrade your HP, the first time it would cost 1 merit, the next 2, the next time 3, and so on. I think there's a limit to the cost for a single upgrade, but I don't remember what the limits are. Mystery Tour has a decent explaination, just go to tips >> merit points.
As for critical hits and recast timers, there are multiple categories that skaw mentioned.
HP/MP(+10 HP/MP per upgrade)
Stats(STR, DEX, etc... +1 per upgrade)
Combat Skills(weapon proficiency, evasion, etc... +2 per upgrade)
Magic Skills(like combat skills, only magic, +2 per upgrade)
Other(your crit rate, enemy's crit rate, plus or minus enmity and something else that I forget at the moment)
Job Specific merits(recast timers and enhanced effects)
Every category other than Job Specifc is available on all jobs at all times. Again, like skaw said, you can only put merits into a job if you have that job at 75 and it's your current main job. Also, those upgrades will only be working when it's your main job, so if you lower your SATA delays, they would only be lowered when you're thf/whatever, it doesn't work if you're /thf. You will also only gain the benefits of the merits if that job is 75, so they do NOT work in level capped areas or if you delevel to 74. I have 2 merits into regen, so my regen spells return 2 more HP per tick, but I found through personal experience that the merits did not work when my whm wasn't 75.
For combat skills, if you raise dagger, you'd increase your maximum dagger cap by 2 points for each upgrade. That'd give you a little better accuracy and damage with each upgrade, so maxing them out you would likely notice. The cool thing about meriting these is that if you put a couple merits into them, you will actually learn weaponskills a level or two earlier than you normally would be able.