I think rogues can work quite well. A few good feat-chains:
1. Dodge, Mobility, Weapon Finesse, Spring Attack
This lets you move into a flanking position attack, and retreat to a safe distance in one round.
1.5 This can be improved with Complete Warrior's Elusive Target
2. Combat Expertise, Improved Feint
This lets you bluff as a move equivalent action and sneak attack without flanking
2.5 If you're playing a high-strength rogue, Improved Trip could be helpful too--it will prevent foes from moving out of a flanked position.
3. Combat Reflexes plus reach weapon (Spiked chain is popular but the longspear requires no feats and rogues don't have a lot of feats to spare). This enables you to take AoOs on attacking foes and increases your flanking options.
4. Two Weapon Fighting, Weapon Finesse, Improved Two Weapon Fighting, etc. If you're going to stay in melee range with a monster, this lets you get off a lot more sneak attacks from a flanking position.
5. Point Blank Shot, Precise Shot, Rapid Shot, Improved Precise Shot.
This really isn't a very good feat chain for a single-classed rogue. (Multiclassed rogues can make it work by relying on strength, favored enemy, and weapon specialization more than sneak attack for damage). There aren't many ways to get ranged sneak attacks on enemies--winning initiative, Greater Invisibility, Blink, Doomtide (the new cleric spell that creates a mist the caster and one other person can see through), and Grease (foes who succeed at the balance check are balancing and lose their dex bonus unless they have 5+ ranks of balance) are about the only ways and you can't count on having them available throughout combat on a regular basis (until high levels).
Some good individual feats:
1. Improved Initiative: This gives you a good chance to go first against quick monsters and an even better chance to go first against slow monsters.
2. Iron Will: Your will save is weak. Counteract it.
3. Great Fortitude: Your fort save is weak. Counteract it. (Unless, of course, you're multiclassing, in which case your fort save may be good).
4. Weapon Focus: +1 to hit never hurt
5. Luck of Heroes: More saves.
6. Strong Soul: Did I mention saves?
7. Improved Buckler Defense (Complete Warrior). Lets you benefit from the buckler you probably wear (you normally benefit from the AC whenever you can't make a full attack) and still attack with two weapons.
8. Improved Shield Bash. If you're a multiclassed rogue with a light shield this lets you keep the AC bonus and get your extra TWF sneak attack damage.
Multiclassing:
Fighter=good. Get extra feats (which you'll want if you're going up several chains of if ). Also, you can potentially get weapon specialization which helps your damage when you can't sneak attack. This is especially helpful for spring attack and two weapon fighting rogues. The fort save is nice too.
Barbarian=good (though you'll need a DM who lets you multi-class INTO barbarian). Fast movement helps the typical skirmisher fighting style, Uncanny dodge stacks, and rage helps a strength based rogue as well. The fort save is nice too.
Ranger=good. You get good skill points and good skills. The fighting styles are nice for flexibility (choosing a style you don't focus in and becoming versatile) or power (saving the feat you would ordinarily spend on two weapon fighting or rapid shot). The fort and reflex saves both help a lot. Choosing Undead as a favored enemy helps to keep you effective against undead.
Wizard= OK. You lose hit points and BAB which hurts but your spells can make you better at your other roles. (Chill touch, for instance, is a great way to deliver sneak attacks). Arcane Trickster is a very nice prestige class too.
The foes that will give you trouble will be undead, constructs, and plants. Fortunately, only undead are often the centerpiece monster of an adventure or campaign. So, find a way to deal with undead. If needed, you can be the tanglefoot bag thrower and general party enabler at low levels and the wand/scroll user at high levels. However, your options aren't limited to that. Since rogues typically have good dex, they will often have the best touch AC in the party--something that means rogues can often hold the line against incorporeal undead better than fighters. (A typical mid level rogue might have a modified dex of 20, a mithral chain shirt, 13 ranks of tumble, and a +1 ring of protection--if he fights defensively, his touch AC is 19--20 if he has dodge and 25 if he uses Combat Expertise too--more if he's in a magic circle vs. evil or if the cleric casts Shield of Faith on him. And, against incorporeal attacks, it's even higher if he uses UMD for shield. That can be hard for a lot of undead to hit. If the cleric gives you a disrupting weapon, you can go to town. You might also want to consider making one of your weapons undead bane. For a relatively cheap enhancement, you can stay in the game against undead. Also consider talking the cleric into casting Imbue with Spell Ability on you. He's going to be spending his time turning and that would let you do some combat healing during that time.