I'm working on this right now... just figured it'd be helpful to know what to expect.
Any gem that vanishes from the board counts (this counts normal gem matches and gems being exploded by special gems).
I've got a "total time played" of 9 hours right now, and "total gems collected of 45,000. So assuming you're as (un)lucky as me, the 45k per 9 hours pace will end up taking about 200 hours to complete.
Math:
1,000,000/45,000 = 22.2 (9 hour chunks)
22.2. * 9 = 200 (total hours)
I'm not a bejeweled wizard, so your numbers might be a bit different depending on luck/skill. I'm also not aware of any cheats or glitches to exploit... just lots of grinding.
Good luck!
UPDATE:
I just hit 100,000 gems collected after 18 hours playing. At the current pace, it'll take about 180 hours. From the comments on this solution and messages I've been getting, it looks like I'm pretty slow :) Others are reporting faster completion times: around 140-150 hours.
UPDATE 2!
I've been bejewling myself into madness. Today i simultaneously hit 2,000,000,000 points, 600,000 gems collected, and 90 hours played.
After some math, I'm getting about 6666 gems/hour, and it should take another 60 hours to get the remaining 400,000 gems. This keeps with the estimate of 150 hours.
Over all this time, I've gotten better at this game... which means I can spot matches faster and keep myself from getting stuck... moving things along more easily. Here are some tips I've learned:
1 ) Always try to work (get matches) from the bottom of the board.
Much of the time, Bejewled is better at Bejewled than you. When you make matches closer to the bottom, there's a greater amount of resulting chaos happening on the board, which causes more cascades. This often results in special gems.
2 ) Given the choice between a vertical and horizontal match, the vertical one is usually better.
If you're not working towards a special gem, taking the vertical matches tends to move things down the board more effectively, which allows you to get back to making matches at the bottom of the board when you're stuck at the top/middle.
3 ) If you're purely going for gems collected, the lightning gems will almost always destroy more than hypercubes.
They always destroy the same amount, regardless of their position on the board. Hypercubes aren't always guaranteed to get a lot, especially if they get accidentally blown up. I tend to try and go for hypercubes just to keep things exciting.
4 ) Blow up special gems immediately.
If you "save up" lots of special gems to make a spectacular explosion, their effects will overlap and you will have wasted much of their potential. "Using" them immediately will maximize their effects. Also try to avoid letting the explosive gems fall to the bottom of the board. if they're at the bottom, the bottom of their explosion is cut off, resulting in 3 less gems collected.
Hope this helps! good luck!
FINAL UPDATE!
Just finished this madness last night. 144 hours.
If you dont already have this game/achievement, do yourself a favor and forget it exists. move on with your life and be happy.