I'm a biiiiig fan of the series. Here's what I'd recommend:
Ys 1 and 2 - Either buy it on VC or Turbo Duo, or get Ys 1 and 2 Eternal for PC and patch it with the translation. Ys 1 and 2 Eternal PC has much much much better graphics, but the VC/Turbo Duo version has much much much better music (which is more important), and is a helluva lot cheaper.
Ys 3 - If you want to play the original side scroller, the Turbo Duo version has the best music, but has choppy parallax scrolling. SNES version has a bit nicer graphics but the music takes a serious hit. Ys 3 isn't that great, but the music is fuck amazing, one of the greatest soundtracks ever in a game. Oath in Felghana is a much better take on Ys 3, it's not a sidescroller but an overhead game. That you can get for PC, and it has a translation available, but the translation is still in beta and never got a public release. But I can hook you up, the translator is a royal prick.
Ys 4 - There are 2 different Ys 4's. The SNES version, Mask of the Sun, which is the 'official' storyline according to Falcom, and the PC Engine version, 'The Dawn of Ys', which is supposedly a million times better. I haven't played Mask of the Sun yet but The Dawn of Ys is my favorite in the series. Mask of the Sun can be played on a SNES emu, a translation is available. The Dawn of Ys can be played on a PC Engine/Turbo Duo, and also has a full translation. Which requires ownership of the original CD game (you can find it on Ebay, that's what I did).
Ys 5 - It's on SNES, but an English translation has yet to be finished. I haven't played this one yet. This and Ys 4: Mask of the Sun are the only 2 games in the series I haven't played through.
Ys: The Ark of Napishtim - Came out on the US PS2, and also US PSP, and Japanese PC. US PS2 is the most accessible version, even though Japanese PC one is supposedly better. Go with the US PS2 version.
Ys Origin - The first Ys that doesn't star Adol. It's a prequel to the whole series. It's available on Japanese PC, but no English translation has been made yet.
http://www.himeyashop.com sells Japanese PC games including the Ys PC games.