3.5? They've been marginalized since OD&D!
Keeping the focus on our 3.5 iteration, there is few if any jobs a rogue can do that a wizard can't do better.
This assumes that a rogue's "job" gets broken down into five major elements: acrobat (movement-based skills), sneak (stealth/recon), face (social skills), dungeon-skills (traps, locks), and striker (sneak attack).
How does the rogue actually fair at these appointed tasks?
* Acrobat: Perhaps the first role a rogue begins to lose at. Just as the rogue is gaining traction with his climb, balance, and jump skills, the wizard gets spider climb (wiz2) and levitate (wiz2) which both make excellent scrolls or wands. Feather Fall (wiz1) is a no brainer anywhere where a fall is possible. Eventually, fly (wiz3) avoids most mundane terrain problems, and dimensional door (wiz4) is a far better get-me-out-of-here power than tumble.
* Sneak: Rogues have one advantage here; no spell easily mimics move silently. However, most wizards have no armor check penalty and typically a high dex, so they aren't exactly noisy like their fighter friends are. Invisibility (wiz2) is far superior to hide; it grants benefits a rogue can't match (no need for cover/concealment) barring HiPS. As for scouting; most divination easily beat spot/listen checks. Detect Secret Doors, Locate Object, and See Invisibility all are amazing rogue-equalizers. Later, Scry and Arcane Eye make mundane recon obsolete.
* Face: Well, a sorcerer has bluff as a class skill, if you still enjoy mundane methods. However, Charm Person, Eagle's Splendor, and Suggestion can all aid hostile negotiations. The disadvantage of failed will saves looms, though.
* Dungeon Skills: Rogues have their only shining star here: Trapfinding. While a cleric has find traps, no other class can find/disable them with regularity. However, there are more than one way to beat a trap! Unseen Servant, Mage Hand, Summon Monster I, or any spell that can circumvent the trap (see acrobat) can stop most mundane traps. Magical traps are subject to dispel magic. Almost any trap is susceptible to a barbarian's greataxe. Knock beats ANY open locks DC. Wizards get decipher script like rogues, for those times when comprehend languages isn't appropriate.
* Striker: No competition. Rogues always lag behind a mage in damage. Rogues need to get flank (which puts them in the thick or melee) or deny foes dex bonus (by spending a round to feint) to deal 1/2 thier rogue level in d6's. Wizards deal that much damage without thought. Magic Missile, Scorching Ray, Lightning Bolt, Force Orb, need I go on? Oh, and all those spells work on undead, elemental, etc. (and any spell without SR, I'm looking at you force orb, affects constructs).
The problem gets exasperated as low-level magic becomes weaker. Once damage-dealing magic from levels 1-3 tap out (max HD, save DCs too low) utility magic discussed above becomes more useful. After-all, there is no effective cap on feather-falls usefulness, long after sleep is a footnote. Magic Item Creation (Scrolls of rarely-used spells, wands, magical items that mimic rogue-abilities (elven cloak, elven boots, ring of evasion, ring of invisibility) start to become feasible to find or make. Prestige classes can make it even worse (Archmage has search as a class skill, a fine skill to skilldump 5 levels in and nearly max out. One level of rogue for trapfinding, and your a better trapfinder than the rogue thanks to that high Int!)
Smart mage-rogues grab permanency: always-on comp languages, detect magic, arcane sight, and see invisibility is a steal for 3,500 (or roughly 2-3 level 10 encounters)
Whats the rogue get all this time? Abilities to keep it alive. Evasion is very nice, but canny mages know touch-attacks (esp. ranged touch) is the way to go. If that doesn't work, target a rogue's low fort or will (esp his will!) saves. Uncanny Dodge is nice but situational; rogues are rarely the #1 target in the opening round and being immune to flank doesn't help when two large monsters are surrounding you (trust me, they don't need that +2 to hit). Trap Sense is very situational (it only works if you failed to do your job properly anyway) and the high level rogue abilities really come too-late to keep rogues viable (1 point of str damage? Wizards were doing 1d6+1 at first level), one extra attack? TWF is much more reliable. 1/2 or nothing? see evasion? Take 10 on a skill? With a few exceptions (tumble, jump, climb, balance, and disable device) you can take 20 with no penalty beyond time. Defensive Roll? Might save your life, but it comes at the time when death is 10x's more likely to come at the end of a save-or-die than a sword blow (or such massive damage the DC for the ref-save is improbable anyway).
The only way a rogue remains viable is if (and only if) the wizard actively chooses not to exclude him. If the wizard chooses not to take advantage of wands of knock, or doesn't keep invisibility prepped (why wouldn't you?) then the rogue can shine. However, that often feels like "mother may I" to the rogue-player; the knowledge the wizard is "holding back" to let you do something can feel mighty condescending.
The other place a rogue can shine is in repetition. Casting knock on every door is tedious, invisibility to scout every hall is consuming. Assuming the wizard doesn't have a cheap way of mimicking the powers needed (wands, etc) then a rogue can do his job over an over. Handy in a dungeon, but if your playstyle doesn't lend itself to a lot of dungeons or long-extended crawls, the wizard at medium-high levels packs more than enough ju-ju to keep abreast with the occasional locked door, the rare "impassable cliff" or the secret door you know is there. In addition, there is no "challenge" in many of those skills: if its REALLY dangerous, than invisibility takes the sting out of failed hide checks, spider climb beats any crumbling wall's DC, and A DC 100 lock is still opened with knock. If there is a real chance of failure, why risk it and instead go with a sure thing?
That's the rogue-conundrum in a nutshell. There is few things a rogue does in a given "scene" that a wizard can't mimic or outshine him in. He gets nothing special a wizard (and his vast array of utility spells) can't match. Its the curse of the mundanes (see fighter) that magic eventually makes the mundane useless, be it masterwork longsword or the rogues that wield them.
