Any time you are going from the wall to a telephone (or modem), you reverse polarity. That is true anytime you are using RJ11 or RJ12. If you are using the flat 4-conductor or 6-conductor cord, put the clip on the same side as the seam in the insulation and it will always be correct. This will change when you go to the RJ45 8-pin plug.
All other times with the exception of connecting two Ethernet ports without a switch, bridge or router you use a straight connection.
Those are used on the 4-pair cat5, cat5a and cat6 cables for Ethernet connections. There are two standards in use and you can use either as long as you use the same wiring on both ends.
Pin T568A T568B
1 W/G W/Orange
2 G/W O/White
3 W/O W/Green
4 Blue Blue
5 W/B W/Blue
6 O/W G/White
7 W/Br W/Brown
8 Br/W Br/White
By the way, just to confuse the issue, the phone company uses yet another configuration, RJ48C, for T1 and E1 lines.