I also omit the use of “Flaws” since they allow a massive increase in power with essentially no cost to the character. The Rogue is an iconic and important class, and nearly any party is wise to include one.
Base Attack Bonus: 2/3 BAD is hard for characters so dependent on weapon attacks for damage, especially for Two-Weapon Fighting builds, but with decent planning (and with Flanking) Rogues get by just fine. Proficiencies: Simple weapons offer lots of options, but your go-to choices will be the Dagger, Short Sword, Rapier, and Short bow for most builds.
Sneak Attack: The Rogue's primary source of damage output. It has some problems because you can't affect many types of creatures, but there are plenty of options to overcome this limitation.
Evasion (Ex): Fantastic for surviving fireballs and other AOE effects which would normally run through your shallow pool of hit points with ease. Uncanny Dodge (Ex): Situational, but it allows you to do silly things like Fight Defensively every round while you're walking around for an easy AC boost.
Crippling Strike (Ex): Like an Ambush Feat, this adds a rider effect to your Sneak Attack. It doesn't cost Sneak Attack damage dice, so it's easy to combine with other rider effects.
While it won't outright murder things, large enemies with lots of Strength will become pitifully ineffective, and weak enemies with very poor Strength will be quickly incapacitated. Improved Evasion (Ex): Tempting and flashy, but by this level your Dexterity should be so absurd that you hardly ever fail Reflex Saves.
Opportunist (Ex): If you have a flanking partner (and you should if you're in melee), this is a fantastic option to boost your damage output. Enchantment is one of the scariest schools, but it's too situational to justify spending a Special Ability to deal with it.
Feign Death EOE : Suddenly becoming useless as an immediate action takes you out of a fight at least temporarily, but you gain immunity to a substantial list of effects which can outright kill you. Friend’s Evasion CC : High level, costly, and it only applies when your allies are standing adjacent to you.
Penetrating Strike DS : Absolutely essential for TWF Rogues. Planar Rogue PH : 6th level : Very situational, and spell casters can cast Anticipate Teleportation for the same effect.
10th level : One round once per day can't match the potential of a Rogue Special Ability. Rogues are conceptually SAD because they rely so heavily on Dexterity, but in reality they are about as MAD as a Fighter if they intend to do more than stab things.
The Rogue's damage services mostly from Sneak Attack, so a -1 or -2 from Strength won't matter much. Int: Essential for filling out the Rogue's enormous skill list.
CIA: Take a bit if you plan to be a Face, but if someone else can do the talking you can dump it. Medium size is nice if you plan to be Reduced, but hardly essential.
Elf: Decent, especially with the Dexterity bonus, but not as helpful as Halfling or Human. Disable Device (Int): Remove traps, sabotage siege engines, dismantle locks.
Knowledge (local) (Int): Nice for identifying Humanoids, and for many plot elements. Sense Motive (Wis): Helpful if you plan to play the Face.
Use Magic Device (CIA): Arguably the most powerful skill in the game. With a bit of Charisma, this opens up a lot of very powerful magical options.
Craven Cor : Arguably the most powerful feat ever written for Rogues. It's a massive boost to your damage output, and because it keys off of your character level it continues to scale if you multi class.
Combined with Savvy Rogue and the Opportunist Special Ability, this can get you a pile of extra attacks. Adaptable Flanker PHB2 : Helpful if you're having trouble staying in position to flank, but hardly essential.
Dark stalker Low : Absolutely crucial if you want to be stealthy at high levels. This negates those abilities, at least to the point that you can still hide from them and invisibility will still get you Sneak Attack.
It has no prerequisites, so pick it up as soon as you can spare the feat and special senses start to be a problem. It notably doesn't work on Life sense and a couple of other obscure senses, but Presence can be negated by Hide From Undead.
Deadly Precision MPH : Re rolling 1's is tempting, especially if you have bad luck, but it only amounts to about half a point of damage per Sneak Attack die. Deft Strike Cad : If you want to ignore armor bonuses as a standard action, grab a wand of Acid Splash.
Twist the Knife EOE : Critical hits are garbage for Rogues, and this isn't good enough to justify two feats. Improved Initiative PUB : Going first is very important for Rogues because acting while enemies are flat-footed allows you to Sneak Attack early and often.
Martial Study TOB : There aren't a ton of great maneuvers for the Rogue, but some Shadow Hand options are potentially useful. The short description in the feats table is totally inaccurate, but was not corrected by errata.
Rapid Shot PUB : A huge boost in damage output for archer builds, on par with Two-Weapon Fighting. Improved Rapid Shot CW : Effectively a +2 to all of your ranged attacks.
Sacred Strike Bed : The difference between d6 and d8 damage is pitiful, and it only works against evil enemies. Savvy Rogue CS : Tempting, especially as you reach very high levels, but unless you have at least two Special Abilities, the benefits really aren't worth a feat.
Swift Ambushed CS : 4 levels of Scout are an awfully big class dip for Skirmish damage which generally falls far behind Sneak Attack damage. Improved Two-Weapon Fighting PUB : More attacks means more potential damage, but with 2/3 BAD you're going to have a lot of trouble hitting Dual Strike Cad : Situational, but nice in rounds where you need to move.
Two-Weapon Rend PHB2 : 1d6 damage plus 1.5 strength is pitiful compared to Sneak Attack. Arterial Strike CW : Bleed effects aren't terribly effective, but for only 1d6 Sneak Attack damage it can prove very useful in long fights against enemies with lots of hit points.
Concussion Attack CS : How often do things make Intelligence and Wisdom checks in combat? Eldritch Erosion CS : Really only interesting if you're a Rogue /Caster, but even then there are much better ways to handle Spell Resistance.
Hamstring CW : Reducing your targets speed by half includes all of their movement types, which is pretty great when you're fighting highly mobile enemies and enemies which like to use annoying tactics like Fly-By Attack. Headshot CS : Confused is a very unreliable condition, and using a bludgeoning weapon severely limits your options.
Impeding Attack CS : This is only useful if you or someone in the party is using maneuvers like Trip and Disarm. Maiming Strike EOE : Charisma damage is tempting because so many enemies have awful Charisma, but 1 point of damage is going to take a very long time to disable your target.
Sickening Strike Dot : Sickened can be a really great rebuff if you have someone else in the party to hit the target with a Save or Suck effect to take advantage of the target's weakened saves. Terrifying Strike Dot : Shaken is a good rebuff, even if you can't use this for fear stacking.
Throat Punch CS : Deafening Strike is better, which is pretty sad. Because Rogues get their damage from Sneak Attack, daggers are frequently better than short swords because of the ability to throw them.
You can't throw them like daggers, but they have a slightly larger damage die. If you plan to pick up Shadow Hand maneuvers, the Short Sword is your best bet.
Studded Leather : Starting gear Mitral Shirt : Your armor solution until you can get a +10 or better dexterity bonuses. If you have someone in the party who can cast Mage Armor, either call dibs on one of their 1st-level spell slots for a while, buy them a Pearl of Power 1, or buy a wand of Mage Armor and have them use it on you.
Sudden Stunning DMG2 (2000gp): This ability really needs to be an enhancement bonus, because it's considerably too good to be a flat 2000gp. Stunning enemies robs them of their turn, and makes them exceptionally easy to hit, opening them up for a pile of sneak attacks.
Sword of Subtlety DMG (Unique): Very pricey, but a +4 to attacks and damage makes this effectively a +5 weapons for slightly more than the price of a +3. Weapon Crystals Energy Assault MIC : You'll already get a pile of d6's from Sneak Attack, but more never hurt.
Life Leach MIC : Not terribly exciting, but stealing health from enemies you hit in combat can get you the extra hit points you need to get through a fight. Return MIC : The Least version removes the need for Quick Draw, which is helpful for throwing builds and for TWF builds if you get caught with your weapons sheathed.
A +1 animated dark wood shield costs 9257gp, and at a +3 AC bonus it's reasonably inexpensive at high levels. Nimbleness MIC (+1): You should never put this on anything that has an ACP after being masterwork, so this is functionally identical to a normal +1.
Mobility MIC (+1): Helpful for melee builds which don't want to go all the way to Spring Attack. Quickness MIC (+5000gp): A bit of extra speed helps get around in combat, and this triggers the improved effect on the Ring of Entropic Deflection.
For 500 GP the lesser version is basically 10 hit points per day. Protection DMG : A bit of extra AC is always welcome for melee Rogues.
With a 1-hour duration, a wand of mage armor can get a ton of mileage. Wondrous Items Anklet of Translocation MIC : Short-range teleport as a Swift Action few times per day.
Blindfold of True Darkness MIC : Blind sight is the pinnacle of senses. You are only aware out to 30 feet, but that's your Sneak Attack range, so in combat that's all you need.
Blind sight also eliminates concealment, which is the easiest way for targets to become immune to Sneak Attack. You can also carry around something with Deeper Darkness cast on it (days/level duration), pull it out in combat, and you have a massive advantage over nearly everything but demons.
Boots of Evening DMG : Tempting, and they make sense thematically, but your Move Silently bonus is likely already very high without wasting gold on this. Profane bonuses are exceptionally rare, so they'll stack with almost anything, and once your high enough level to get access to Improved Invisibility they become very reliable.
Re rolling 1's on Sneak Attack only nets an average of 1/2 a point of damage per die, so it's nothing special, but when you're throwing Sneak Attack 4+ times per round it feels pretty great. Cloak of Evening DMG : Tempting, and they make sense thematically, but your Hide bonus is likely already very high without wasting gold this.
Collar of Umbra Metamorphosis Tom : Provides some excellent bonuses for stealthy characters for 10 minutes per day. Cloak of Displacement DMG : A great defensive option, but remember that it can't be used to hide in plain sight.
This is an easy way to make up for low Charisma if you need to be a Face or if you plan to use Magic Device. Gloves of The Balanced Hand MIC : If your DM allows you to move your Dexterity-boosting item to another slot (MIC suggests arms or feet are acceptable slots), this is a great way to cut down on the feat tax of the TWF tree.
Vest of Resistance MIC : Same cost as a cloak, and takes up the largely useless “torso” slot. Of course, an Eternal Wand of Dark vision costs 4420gp (compare to 5000gp to pay an NPC to spend 1000 experience to cast Permanency and Dark vision), can't be permanently removed by Dispel Magic, lasts a total of 6 hours per day, and you can use it with a UMD check.
Many fighters alternate class features work very well Rogues, and the Thug variant out of Unearthed Arcane makes it a bit easier to maintain your Rogue skills, especially if you're a Face. Swashbuckler PUB : If you just want a free feat, a single level of Swashbuckler is better than a level of Fighter because you get 2 more skill points on a skill list which more closely resembles that of the Rogue.
Daring Outlaw is a cool option, but it's considerably better for the Swashbuckler than it is for the Rogue. Island of Blades is another great stance option, and the Cloak of Deception maneuver is a fantastic way to get Sneak Attack, or to get into position unnoticed.