I don't think it's a "waste" of skill points. In fact, I'm not certain that skill points can be wasted.
What can be done with them is that you can use them to create improbable or ineffective characters.
Is a gnome illusionist with 4 ranks of profession: Farmer more or less believable than a gnome illusionist with 1 rank of Craft: alchemy, one rank of profession: farmer, and two extra points of concentration or spellcraft? The gnome with four ranks was very dedicated to his farming and learned everything he could about it during his early years. The other gnome only learned what he couldn't avoid learning--he spent other time mixing potions and antidotes to feed to the animals and reciting his spells backwards while milking the cows. The first gnome probably had to be forced out of farming. The second gnome dreamed of a different life--a life of adventure. Which description fits your gnome better? If it's gnome number two, then you didn't "waste" 3 skill points on background skills--you failed to make your character and the mechanics that represent him match up.
Now, there are characters who aren't adventurers. The 6 str rogue who spent all his skill points in profession: merchant, bluff, diplomacy, sense motive, and cross-class ranks in Knowledge: Nobility and Royalty, Knowledge: Local, and Knowledge: Geography and then used his feats to be better at trading grain and coordinating caravans is not going to be a very good character in a traditional D&D game (and probably won't be useful in any D&D game unless it's exceptionally light in combat). In that case, the real question is not, "did the merchant's player waste his skillpoints on 'background' skills that don't make him combat effective?" Instead it's "why did the player choose to play a character who is useless in combat instead of one who isn't a drain on the party?" And the related question is this: "What is Mr. Merchant doing in a party of adventurers? That character should be looking for another line of work."
If you're playing Drizz't Do'Urden, Hide, Tumble, and move silently ARE background skills. And Two Weapon fighting and weapon focus: scimitar are background feats. If you're playing Clint Eastwood's character from Unforgiven, Quickdraw, weapon focus, point blank shot, rapid shot, precise shot, and far shot ARE background feats and Sense Motive, Handle Animal, Ride, Spot, Listen, and Intimidate ARE background skills. So the question isn't "should I waste skill points on background skills or maximize my combat effectiveness?" Instead, it's "will the campaign support a combat ineffective character concept?" (And, in most D&D games, the answer is "no." Suboptimal? "probably. . . unless everyone else is hyper-optimized.")
