I think i'll avoid using multiple entries from a single series with one exception.
1. The Legend of Zelda: Ocarina of Time- It may be a choice that lacks much in the way of surprise but theres good reason it tops so many lists like this. While there are many quality Zelda games I still feel that Ocarina is the one that truly manages to strike the best balance between all the features one expects from a Zelda game. Id say that TP has better dungeons, WW has better art direction, Alttp has better music, MM has the best world in itself and I could go on. But OoT manages to bridge all these various aspects together to make the most cohesive Zelda game with perfect pacing, all those other entries fall short in other areas but Ocarina feels well rounded enough that there is little for me belittle, the 3DS remake being the best version available.
2. Donkey Kong Country 2- Delivering great settings, inventive level design, solid gameplay and a stunning soundtrack, together these elements form what is my favourite platformer. A massive step up over the original DKC, this sequel manages to make every stage feel unique, each with their own hook. Nothing is placed without reason, secrets are all over the place, if you spy a lone banana sitting in a bramble wall then you can be assured its no error, its the sign that doing something usually foolish like leaping face first into a bramble barrier is in fact the path to a hidden item and fortunately they dont go overboard with the collectables so that it detracts from the experience. Mario may have the more fine tuned platforming but the sum of this games parts elevate it to a higher status for me. And it bears repeating that this game has a soundtrack of the Gods.
3. Super Mario Galaxy 2- And here is my favourite 3D platformer, expanding upon the already brilliant original with more suits, more difficulty, more Yoshi, more stars and so on in that fashion. While it is incredibly similar to the first game to the point it could be an expansion pack its fantastic stage design ensures that it rises above that somewhat demeaning moniker and gives it true sequel status.
4. Metroid Prime- A world oozing with atmosphere, filled with hostile life forms and conveniently a bunch of items that work well for the lone heroine whos arrived in pursuit of some shady Space pirate activities. You dont have much to go on but you dont need to, to discover things for yourself is part of the experience whether its the history of Tallon IV obtained from scanning lore or the many items that are scattered across the planet.
5. Super Mario World- Id say that this is probably the best platforming game Ive played from a purely mechanical standpoint, the level of control you have over Mario himself is sublime and that alone feels like enough of a reason to rank this highly. But things dont stop there what with the brilliant stages, hidden exits, exhilarating cape flight and a Yoshi with an insatiable appetite. Pure gaming bliss.
6. Pokemon Fire Red- The nostalgia runs strong with this one, while Black and White are probably the best the series have to offer I cant deny myself a trip to Kanto with the original pokemon, fortunately the game got a much needed update with the GBA that makes it easily playable today and as a bonus it plays much faster than any other pokemon game if Im not mistaken. The formula is a classic one that continues to work, creating your own team is one of those joyful experiences, the moment when you have a dream team of 6 fully evolved battling machines is one that is hard to top.
7. Fire Emblem Path Of Radiance- Another game that involves forming a team that kicks ass and takes names in such a way that it makes Reggie proud. But in Fire Emblem your team are in more of a bind than most games as their very lives hang in the balance of your leadership, a unit thats been with you through many trials could fall victim to an unexpected critical hit and unlike pokemon they dont faint, they die. As such units dont feel expendable and Ill be damned if Im going to lose my comrades. As for PoR itself Id say it has a stronger plot than any other of the international release FE games with better characters to boot.
8. Perfect Dark- So since Rare games from the N64 era count I have to make mention for my favourite FPS game, surpassing the solid groundwork laid by Goldeneye. For its time the content in this game is incredible, a single player campaign with fully voiced cutscenes (hey for the N64 this is great!) that has stages that could change over the different difficulty levels and added plenty of extra objectives, co-op mode, counter-op and those oh so enjoyable cheats. A vast lineup of weaponry and gadgets that have multiple functions. A multiplayer mode with many maps including some Goldeneye classics, simulants with varying personality types, character stat tracking, robust music options, being able to save gameplay settings and challenges
..okay Ill stop now.
9. Xenoblade- A recent entry but a damn good one, a JRPG that manages to stand out among the jumble of seemingly polarizing games in the genre from recent years . Rewarding exploration in a huge world and bringing an interesting battle system to the table with a mammoth soundtrack. An unexpected gem and one of the very best games on the wii.
10. Super Smash Bros Brawl- For some reason the Smash series often slips my mind when it comes to times like this despite the fact that Ive put an absolute ton of hours into all 3 games. Probably because Im still waiting for one entry to finally have all the characters I want. That aside the unique style of fighting gameplay on display in this series is an enjoyable and chaotic twist on the standard. As for the selection of Brawl, the character roster is my favourite of the three which is what counts the most to me.
Honourable Mentions
A barrage of DS games like Elite Beat Agents and Kirby Power Paintbrush, other great entries in already represented series like DKCR, Majora's Mask, Super Metroid and Super Mario 64. Mario Kart DS, Mario and Luigi Superstar Saga, Banjo Kazooie, F-Zero GX and Lylat Wars. Okay this has become a top 20 now.