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.
As part of the Appraise skill description in Rules of the game, it is true that rare items are made by craft with appropriate skills between +10 and +14 and it is also true that the masterwork component of a weapon is DC20 thus a skill modifier of +10 on a take 10 required for the crafter. But the Appraise skill is used to determine the value of an item not its nature. ie. a longsword that is worth 315 gp maybe a masterwork longsword or a ceremonial longsword (used as a normal longsword in combat). If we consider this, we could even adjudicate that someone with an appraise skill could not determine if it is a masterwork item but only that it is worth that much. A rusted/damaged masterwork longsword could be valued at 200 gp instead of the 315gp with an appraise check. On the other hand, someone with a craft skill in the appropriate craft has to recognize something he can do. The crafter would know it's a masterwork weapon, that it is damaged but won't be able to give a value of the item.

Also, it is not clear if appraise can be used on items at all as weapons are defined as weapons and armors as armors in rule books while items are all other objects.

When looking into the Player's Handbook, Dungeon Master's Book and Rules Compendium, there is no rule that states how to recognize a weapon, an exotic weapon or a masterwork weapon. The only rule that exists is for magic weapons that can't be determined unless with something similar to detect magic. 
The question is very valid but I can't see anything in the rules that would stop a character to recognize a masterwork item, the same as to recognize an exotic weapon, etc. At this point I would recommend leaving this to the DM to decide and take into consideration that a character with the weapon proficiency should know how to recognize a weapon he can wield and probably a masterwork version by handling it or by seeing someone handling it. And someone with the craft skill modifier of +10 should also be able to recognize a masterwork weapon. You can easily use the DM option of using skills with different modifiers such as a spot check with Int modifier that needs to beat the craft DC. But this is really an example. As long as it is not used to unbalance the game that you decide it is not possible to know or that the PC know automatically. (i. e. if they can't know, then the Sunder combat option for the PC is less interesting since it means they will potentially break and render worthless their loot. On the other hand, you may discover that always knowing and having your barbarians PC take Improved Sunder and Power Attack to break all weapons that are not masterwork will get too much gp value with the masterwork weapons collected to the groul, then you can easily add the "damaged weapon lesser value" that appraise will be used to figure out... or not let them know).

Good question, not sure the answer is what you were looking for but ultimately, it's yours and your players' game.