Here's the rogue-specific macros I'm currently using, in my Combat spec:
To Apply Poisons:
#showtooltip Instant Poison
/use [button:1] Instant Poison
/use [button:2] Deadly Poison
/use [button:3] Instant Poison
/use [button:1] 16; [button:2] 17; [button:3] 18
/click StaticPopup1Button1
#showtooltip Wound Poison
/use [button:1] Wound Poison
/use [button:2] Crippling Poison
/use [button:3] Crippling Poison
/use [button:1] 16; [button:2] 17; [button:3] 18
/click StaticPopup1Button1
These two macros make it easy for me to poison up. With both macros, I left-click to apply the poison to my main hand weapon, right-click to apply it to my offhand weapon, and middle-click to apply poison to my Thrown weapon. The first macro is for my PvE poisons, and the second is for my PvP poisons (Actually, I'm just using PvE poisons for PvP nowadays, thanks to talents in my tree that slow down enemies). Any other poisons I just apply manually on an as-needed basis. So, for example, before the heroic or raid starts, I'd right-click the first macro button to apply Deadly Poison to my OH, left-click the same button to put Instant on my MH, and middle-click to put Instant on my Thrown (for Fan of Knives).
The last line in the macro will take care of the "Would you like to replace your current poison?" dialog box.
To bind an on-use trinket to Blade Flurry:
#showtooltip Blade Flurry
/use Mark of Supremacy
/startattack
/cast Blade Flurry
Since the Mark of Supremacy shares its cooldown with Blade Flurry, I've set up a macro to tie them together, so that I don't forget to use the trinket. Note that if you click the macro button when you're still on your Global Cooldown, it will pop the trinket without popping Blade Flurry. In order to compensate for this, I tap the button a few times until I'm sure they're both activated.
Tricks of the Trade: Focus
#showtooltip Tricks of the Trade
/cast [button:1, help] [button:1, target=focus, help] [button:1, target=targettarget, help] Tricks of the Trade
/focus [button:2, help]
/clearfocus [button:2, noexists]
For my Tricks of the Trade, I will set a tank as my focus at the beginning of the run by selecting the tank from the group, and right-clicking this button to set them as my focus. (Right-clicking without a target clears the focus at the end of the run.) Then, when I need to cast Tricks of the Trade, I just click the button to set it on my focused tank. (If there isn't a focus, it'll set it on the mob's current target, or if the target is friendly, it'll set it on them.) This macro, however, doesn't work if I enter a fight with a friendly NPC targetted, such as when I had just talked to Arthas in the second half of Culling of Stratholme to get him moving.
Tricks of the Trade: Current Target
#showtooltip Tricks of the Trade
/cast [target=targettarget] Tricks of the Trade
I just started using this macro for a second Tricks of the Trade button, which simply casts Tricks on the current target of the enemy. This one's handy for tank swap fights where you'd like to cast Tricks on the current tank, whoever that is. With the T10 2-set bonus, this macro comes in handy.
A better, spammable Sap:
#showtooltip Sap
/console targetNearestDistance 10,000000
/targetenemy [noharm][dead]
/console targetNearestDistance 41.000000
/cast [harm,nodead] Sap
I'll admit that I don't know how this one works, but it's great to spam if there's a stealthed rogue nearby, because it'll increase your chances of sapping them before they sap you.
My StartAttack Macros:
#showtooltop Fan of Knives
/cleartarget [dead]
/startattack
/cast Fan of Knives
#showtooltip Killing Spree
/cleartarget [dead]
/startattack
/cast Killing Spree
#showtooltip Sinister Strike
/cleartarget [dead]
/startattack
/cast Sinister Strike
I've created these macros to make sure I've got a current enemy target whenever I use one of those abilities, in order to maximize DPS. Even when I'm spamming Fan of Knives, I position myself to also be attacking a target at the same time, and the macro will pick up a new target for me when my current target dies.
...and a StopAttack macro:
#showtooltip Vanish
/stopattack
/cast Vanish
This macro just makes sure I don't attack anyone after I Vanish, which would take me out of Vanish. It might or might not be obsolete because I've used it for ages, but I still use it.
Spamming Pick Pocket for Profit!
#showtooltip Pick Pocket
/cleartarget
/console targetNearestDistance 8,000000
/targetenemy [noharm][dead]
/cast Pick Pocket
This macro will pick the pocket of whoever's in front of you, even if they're not currently targeted. Use this with the Glyph of Pick Pocket, and you can run around picking pockets to your heart's content (great for working on The Insane in BRD, or collecting valuable Flame-Scarred Junkboxes). The mob whose pocket you last picked will be the target after pressing the button, so you know whose pocket you just picked.