As a new rogue gearing for PvE, I used mostly the following gems:
Red
======
Glinting Noble Topaz (4hit / 4 agi)
Bright Living Ruby (16ap)
Yellow
======
Rigid Dawnstone (8hit)
Blue
======
Balanced Nightseye (8ap / 6 stam)
Shifting Nightseye (4agi / 6 stam)
The blues were kind of a toss up for me, and the reds I went with the glinting topaz at all times except for a couple sockets where I was just lazy and had some living rubies on my JC that I wanted to use up. For PvE progression, +Hit is your friend until you have the gear to support stacking other stats in it's place.