Rupees are (according to wikipedia) the currency used in India, Sri Lanka, Nepal, Pakistan, Mauritius, Seychelles, Indonesia, Maldives, and formerly in Burma, and Afghanistan. Rupees of these countries do not appear as we know them in Hyrule.
Though there are a variety of colors in the real life rupees they seem to be similar to what we would consider dollars in coins and bills. Personally I think the multi-color gems stones in varying sizes is way cooler
As to whether or not this was intended to be a reference to real life in anyway, I doubt highly. I do suppose it is possible, but I do not have enough knowledge on the subject to make a good guess or theory.
Rupees are an interesting aspect to Zelda that I think have some importance in some games a little to no importance in other games. For example, I found that in game like OoT where you could find rupees almost anywhere and there was little to no use for them, that they were redundant and almost unnecessary. I found on many occasion that I am at the highest number of rupees I can carry. Rupees in OoT are very common to find and build up in your inventory. Now, this would be beneficial if there was some use for them. But in this game, there is not. Most items (arrows, bombs, deku seeds, etc.) can be found by cutting grass or killing enemies. Therefore, there is no need to go to any of the numerous shops around Hyrule to purchase them, leaving your wallet full. The only instance in the game where rupees are really required is to play the mini games, most of which only cost 10 rupees, and the Happy Mask Shop sidequest which conveniently ends with your wallet being filled to the breaking point. Further, most of the high profile and required items in the game are given to Link for free in the temples or the overworld. Required items that can be purchased for the most part are able to be found in the overworld anyway. The example being the Hylian shield in the graveyard (as apposed to buying it in the bazar). Of course there is exception to this with the deku shield, however, this occurs at the very begining of the game and there are more than enough rupees laying around the Kokiri forest to get the required amount in record time. In this regard I find them to be a backseat item of little importance to the game as their use is limited and number abundant.
Conversely, Twilight Princess made use of the rupees. They were still as abundant and items were still able to be found in the bushes, grass, under rocks and in chests, but they had many more uses. More sidequests required them including fixing the bridge to Castle Town, donating to the Malo Mart fund, and the usual minigames, but most of all they had an ultimate purpose: Magic armor. The item sucked rupees like a nobody's business which ultimately resulted in a major loss of them. This caused this item to seem more rare and certainly made it more valuable. Giving the item a larger and more important use make it important to the game. OoT lacked this need, and thus this is the difference between the two games and the rupees.
Majora's Mask's use of rupees lies somewhere in the middle. Rupees were easy to get and abundant and they also had little use, but they were taken away from you at the end of every three day cycle. In this sense they were more rare than in OoT, but not as functional as in TP. Now, Mm did bring an interesting mechanic to the table regarding rupees in the bank scenario. Loosing rupees was in some way annoying if you did need a couple to buy the odd thing or try to beat the shooting gallery for the 20th time, but the bank allowed you to save your rupees and therefore have access to them if you did need them for one reason or another. This mechanic contributed both to the rarity of the item and to the the abundance. Rupees were always at your disposal if needed, but, in trying to fill the bank to get the heart piece, finding rupees in the overworld became an important task. My opinion on this is that, the single task of getting enough rupees to obtain the heart piece does not contribute to the overall use of rupees for the game. I still feel that rupees were under used and a rather irrelevant item in this game (as well as OoT).