Wow, there are so many.
Standard bombs are great, if not a little boring at times. I love to use them as a weapon though, and I love how they are in, I belive every Zelda except AoL. One of my favourite uses of them, ingame was the bomb shop in WW. I absolutely loved how they were like 30,000 rupees for 30. I just liked the sense of realism there. Another of those great realistic moments
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The water bombs were really cool, but I didn't like the idea of making a whole new type of bomb for just one function. It was really cool though to suddenly discover that there were all these blow-upable rocks underwater that would give you Rupees and even a new bomb bag
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The Bomblings in TP were utterly useless. I honestly have never used one.
The Bombchus were useless and rubbish in OoT, they were inaccurate and you basically only ever needed them in the Bombchu bowling alley, which I'll admit, was a hell of alot of fun. However, the Bombchus in PH were brilliant! They had so many uses and they really did help alot in situations such as trying to take out the odd Phantom's Eye. Also, I really liked how there were areas in this game that you could only get to, or only activate if you had the Bombchus, and I really liked that they created a big shortcut in the Temple of the Ocean King.
The Bomb Arrows were also awesome. Blowing things up from a distance? Genius! I remember getting them and thinking it was useless. Some time after I had to escort the carridge which contained Ilia to Kakariko, and realised how useful they were against those stupid Twilight-bird-things that kept attacking. Then shortly after that, in Kakariko Village, I remember looking up and seeing those boulders, shooting them with my Bomb Arrows and getting a heart piece! Thar's when I realised how great Bomb Arrows were.
Another really cool item was the Super Bomb in ALttP. However, it had an incredibly limited use and it was very annoying that it would stop if you ran using the pegasis boots. On the other hand though, the short part that it did play, was a seriously awesome one.
My all time favourite though, would absolutely HAVE to be the remote bombs in MC. I loved how they were portrayed as legendary in Swiftblades Gossip Column, and it was such an original idea. They were also so useful for those damn rooms where you had to blow everything up at an exact time. I really really hope that the Remote Bombs make a return. REMOTE BOMBS FTW!