Question: Can a weapon wielded during combat be immediately identified as a masterwork weapon simply by looking at it, or does it require some sort of search, appraise, craft(weaponsmithing) or some other ways to see that it is in fact a masterwork weapon ?

Answer: 
Definitely not. Even with a skill check, it's not plausible to gauge the quality of a weapon just from a glance. The characteristics that make a weapon effective as a weapon (balance, metallurgy, etc. etc.) aren't visible to the eye, or not without close inspection. (Exception: special materials may or may not be easily recognisable.)

If the weapon is distinctive, you *might* be able to make an educated guess: "only the Iron Dwarves make their axe-heads in that shape, and they're famous for the quality of their work". But that would definitely require a skill check (IMHO Appraise or Craft) and you might get fooled if somebody's making cheap knock-offs in the same style.
I think weapons can have various visible qualities that rule out the possibility of them being considered masterwork: notches in the blade, bends where things should be straight, and so on. As a DM, I would probably use signs of poor maintenance, like rust, as a sign of low quality weapons—after all, even though you *can* fail to give a quality weapon proper maintenance, that’s not expected in this game where equipment maintenance is hand-waved as assumed to be happening in the background.

But plenty of other things can be wrong with a weapon that aren’t obvious just by seeing the weapon at a distance. Issues with balance and weighting, for example. Maybe portions of it haven’t been hardened properly. Whatever. It seems easily plausible that a weapon could fail to live up to the standards of “masterwork,” without actually having any visible defects.

And then, on the flip side, there are certain things in the rules that are always applied solely to masterwork weapons. Most special materials, for example, specify that weapons made from that material are always masterwork. If the material can be recognized, then you can tell it’s masterwork. Likewise, certain distinctive styles might be renowned as always of the highest quality—for example, officially katanas are statted as “bastard swords that are always masterwork.” So if you see a katana, you knew it was masterwork. Similar things might be true in a given campaign world for elven or dwarven or whatever weaponry, perhaps.

Finally, of course, magic weapons are always masterwork. Someone with *detect magic* or similar could therefore recognize masterwork weapons when they are also magical.

So the long and short of it is that there are some weapons that are clearly not masterwork, and other weapons that clearly are masterwork, and then a decent chunk of weapons that cannot be directly determined by visual inspection.

The other thing worth pointing out here is that D&D 3.5e has really minimal rules for “sizing up” your opponents, at least in martial endeavors. There is no martial analogue to Spellcraft, for example. Many tables play this straight, forcing players to learn about their opponents by making rolls and seeing what is good enough and what is not, for example, to gauge their AC. If the DM rolls opponent rolls openly, attack roll and saving throw bonuses can also be found this way. The problem with this is that you only get to see so many rolls before the fight is decided: it is rare for a fight to go more than 2-3 rounds without a clear victor having emerged (even if mopping up is often necessary). Too much happens on a given turn, in a given round, for this method to really be all that effective.

It’s also not realistic. Warriors are much better at sizing opponents up—at least in the sense of, “better than me,” “worse than me,” “about equal,” “*much* better than me,” and so on. Obviously, the real world doesn’t boil everything down to nice, neat numbers, but “getting the measure” of your opponent is a thing—that phrase, along with “sizing someone up,” is a phrase because it describes a real process.

So a warrior might not be able to tell how high-quality a weapon is at a glance, but he *will* be able to tell, very quickly, to a general degree how high-quality his opponent is. That gives hints about the quality of his equipment. An opponent *might* have been caught off-guard, and be using whatever weapon he had at hand, or somehow have recently lost his best equipment for some reason, but *most* of the time, a high-quality opponent is likely to have high-quality gear. After all, a masterwork weapon is easily affordable by 2nd level, even on NPC wealth, and well worth it for anyone who plans on hitting anyone with a weapon. Really only 1st-level characters should have non-masterwork weapons—and even most of those will still have the masterwork version.