So here's my story.

When I was a kid our family could only afford one game system and a couple of games to go with it. Here's what I owned:

NES

Super Mario Bros, Kung Fu, Wrestling

Genesis

Sonic 1 and 2, Streets of Rage, Golden Axe, Columns, some sports games.

As yo can see I missed out on a lot of games and the whole SNES library. Now that I'm older I really want to play these games, however my wallet isn't particularly fat right now nor will it be in the short term future. I already made a list of the games I want play and they're all fairly popular games. Since I don't own any retro consoles my plan was to buy the Retron3(along with 2 controllers for each console) and buy the games on ebay or something similar. I don't want to start a game collection, my intention is to buy games that I plan on playing.Based on your experiences, is it difficult to find games for the NES, SNES and Genesis fairly cheaply and in good condition?

My other plan is to buy a really good gamepad for my PC and play the games using emulators. Honestly, which route is safer and will give me the most satisfaction?

I would just use an emulator, it's less work for it and cheaper. I use it for GBA games all the time and it works great for me.

to play the games legally, I would use the Wii's Virtual Console and to a lesser degree PSN.

 I would advise the following for the Virtual Console:

Secret of Mana

Super Metroid

Super Mario RPG

DKC 1 - 3

Super Castlevania IV and Rondo of Blood

Super Mario Bros 1 - 3 

Super Mario World

Gunstar Heroes

Final Fantasies I and IV

Mario Kart 64

Zelda ALttP, OoT and MM

Paper Mario

Ogre Battle MotBQ and 64

Super Mario 64

Sin and Punishment

Phantasy Star I to IV

Ristar

Shining Force 1 and 2

use an emulator and plug in your ps3 controller.  its a little difficult to get working because sony hasnt made pc drivers for it, but if you just google it you can get it working fairly easy

For the mega drive (genesis)

I would go:

Altered beast

Toe jam and earl

Afterburner II

Sonic 1 and Columns and Sonic 2 because that is where he has the down a fast bit. Sonic 1 would have been a whole lot different with that.

Alien storm

I have more  but that should get you started :D

With an emulator such as ZSNES and google sites for SNES roms. For SNES games, I have found a keyboard works really well until you get into fighting games. Any other game you can play just fine.

I would not go amazon or ebay for this stuff. Way overpriced because they are collector's items now. For example, a brand new, original addition of Earthbound in it's big box with the scratch n' sniff strategy guide was bidding for over $450 on ebay. Lord knows what a semi new SNES system is going for nowadays.

Remember the good times for what they were and move on. Obviously that is my take, my experience is we tend to have some rose tinted glasses when it comes to remembering games of our youth. I have some good memories but modern repeat experiences have always been less than satisfactory.

I played the sega mega drive collection with absolute glee so each to their own :)

True, but the problem I never played any of these games, so it would be the first time playing them.