The basic concept behind theorycrafting (will now be referred to as "TC'ing") is to minimize or maximize something. You'll hear it called "min/maxing"; the idea is to raise a desired value and to decrease an undesirable value. An example is Attack Power: it is often considered the most important statistic for a PvP Rogue and can generally be used to gauge the gear level of the Rogue in question. Something you may wish to minimize is your chance to miss: hitting more often is the core behind every Combat raider's gear and talent choices.
The way to properly determine which path to take is to break each path into its fundamental parts, and to then compare the parts. Looking at two items with different stats can become very tricky, so by converting them to the core stats (Attack Power, Critical Strike Rating, etc) you can greatly simplify the process. The hardest part of TC'ing is to properly disassemble the elements while considering things like buffs, debuffs, party members, and the target you're attacking.
A quick example of how to break down stats on items:
Ring of Strength: +15 STR
Ring of Attack Power: +15 AP
For a Rogue, 1 STR is equal to 1 AP and so these rings provide exactly the same benefit, barring outside influences. Using the basic formulae for Attack Power and for Critical Strike will allow you to break down any item in game. The core values for DPS are traditionally thought of as: Attack Power, Critical Strike, Hit, Expertise, Haste, and the newly-revamped Armor Penetration. Let's take a very controversial example of gear choices and look at the theorycrafting that goes on behind the scenes.
Two new sets of leather PvP bracers became available for Honor Points in patch 2.4.2, Guardian's Leather Bracers and Guardian's Dragonhide Bracers. They're available to both Rogues and Druids, with the first being tailored towards Rogues and the latter designed for our kitty cat friends. You'll see a large split between Rogues on which they decide to pick up.
In order to evaluate what pair trumps the other, we'll have to use the basic stat formulae that I mentioned above. I will break down this first example in detail. 1 point of Agility converts to 1 Attack Power and 0.552 Critical Strike Rating. 1 point of Strength converts to 1 Attack Power. We convert these stats, and then add them up together.
Dragonhide: 50 AP, 33 STAM, 17 RES, 38 CRIT, Red Socket w/ 2 RES bonus.
Leather: 60 AP, 37 STAM, 15 RES, 30.5 CRIT, Yellow Socket w/ 2 RES bonus.
The simplest way to start is to only focus on the differences between the sets. So, we'll remove all the stats that are the same on both items and remove the defensive stats (stamina and resilience), because they are similar and most Rogues focus on damage anyway. To make comparison easier, let's consider a situation where a Rogue is playing by himself, with no outside buffs or influences. Here's what the difference comes out to be:
Dragonhide: 7.5 CRIT, Red Socket
Leather: 10 AP, Yellow Socket
If we use Blizzard's iLVL scale, AP is typically valued at 2x the value of Critical Strike Rating, as seen by the gems for AP when comparied with the gems for Critical Strike Rating. This would put the Dragonhide Bracers significantly ahead, as the 7.5 Critical Strike Rating is worth 15 AP. However, this scale is largely inaccurate: it fails to compensate for talents, buffs, and specific playstyles.
For example, many Rogues will have the talent Sinister Calling, which increases their Agility by 15%; and also Deadliness, which increases their Attack Power by 10%. Considering that the Guardian's Leather Bracers have more Agility and pure Attack Power, this will mean they see increased benefit from the talents. Let's reexamine both pieces from the perspective of a Rogue with these talents. I converted Strength and Agility to their raw stats beforehand, removed the unimportant defensive stats, and factored in the two talents. The difference between them comes out to be:
Dragonhide: 7.25 CRIT
Leather: 11.5 AP
You'll see that while the AP and Critical Strike Rating on the Leather Bracers scaled better with the deep Subtlety talents. Now, in order to determine which is more valuable, the AP or the Crit, you'll have to figure out which increases your overall DPS by a greater amount. The key is to remember to evaluate your talents, buffs, and opponents when TC'ing to ensure that your results point to the correct choice. For example, a player that takes less damage from Critical Strikes will make AP more valuable; while a Rogue who has talents that proc on crits like Seal Fate and the brand new Focused Attacks will see the balance ratio tip away from AP.
Focusing on every stat and hoping you remember which talents affect what and so forth can get out of hand very quickly. Luckily, some of the fantastic Rogues over at Elitist Jerks (my favorite community for theorycrafting) have worked up a DPS Spreadsheet. What this allows you to do is easily plug in your gear and talents, and it will do all the math for you. You can then experiment changing talents, regemming, and enchant choices; it will show you if your damage will go up or down. This is perfect for trying to decide whether a piece of a gear is an upgrade for you, or which piece to upgrade first.
It does take some getting used to and some initial startup time, but once you have your character's information entered into the spreadsheet, it is trivial to test new builds and gear without even having to log in. While none of this theorycrafting stuff is worth more than actual in-game testing, it can give you a very good idea of which way to go when deciding between Find Weakness and Focused Attacks or between buying your Season 2 helm or chest first.
Ultimately, if your goal is to do the best DPS you can, you're going to have to theorycraft every piece of gear, every talent choice, and every ability that you use at any given time. WoW can easily become a math game, and unfortunately for us Rogues, there is a "right answer". However, it's also important to remember that it IS a game, and that sometimes you have to worry less about that last 1% of DPS and start trying to have some fun.
So what if that sword that dropped is an upgrade: you like the look of your Heartless! I'll admit that my Warlock used the Argent Avenger with a Strength Enchant on it; and I took that sword and raided from Molten Core to Ahn'Qiraj. I got invited to more raids because I was "that Warlock who uses Rogue weapons" rather than because I did more DPS than anyone on the server. Try to balance being "all you can be" against "have some fun" and I'm sure you'll find a happy medium where your guild is content with your damage and you get to play in a way that you actually enjoy.