I'm a light gun fanatic and have all the guns asked about here (+ loads of others)...
I'd skip Aimtraks. I've never got the firmware working on my PS2 and they suck on my PC anyway. It's a terrible product and way too expensive. Mine live in a draw unused).
The EMS Topgun 3 works on a PS2 console (as a guncon 2) and a PC + original Xbox. They work on HD flat screens. They're OK but glitchy.
Backwards compatible PS3s essentially become a PS2 when playing PS2 discs. No PS3 accessories will work. The guncon 2 works but only for PS2 games.
The PS Move is a terrible lightgun. I'd rather not play at all than use my Move. It constantly loses calibration. Just don't...
The only light gun game that can't be played elsewhere on the PS3 is the Time Crisis 4 / Razing Storm disc. This is best played with a Guncon 3. The GC3 is not bad for a camera based gun but it only works for 3 games... Basically, forget the PS3 for gun games unless you love TC4.
The Wii remote is also terrible as a gun. Wii gun games are best played in the Dolphin emulator for this reason. I own a Wii console but still use my PC with Dolphin for shooters so I can use my Sega arcade IR guns and my USB2Gun (with real light guns).
The new Sinden light guns for a Windows PC are apparently pretty good. I haven't tried them as I chose to invest in real arcade guns instead but I'd give them a look if you're on a budget.
I recommend using a real PS2 console and PC. Grab a PS2 with the official Namco Guncon 2 + a cheap (or free) CRT tv off Craigslist. The PS2 is the best home light gun system ever. For everything else, I'd recommend PC with a Sinden or real Sega arcade guns.
There's a lot of awesome new light gun content that has become playable on a PC lately. You have a lot of the latest arcade shooters like House of the Dead 4, Rambo, Golden Gun, Transformers, Too Spicy etc via Teknoparrot.
You have other cracked PC based arcades like Time Crisis 5, Virtua Cop 3 and Operation Ghost too. It's a great time to invest in a set of decent recoil guns+.
BTW, free mcboot and mod chips offer no additional controller compatibility benefits for PS2 consoles. The only mods I've ever seen in this area are some game patches to make old PS1 titles compatible with a GC2 or GC1 gun (instead of the old Konami guns).
That's my $0.02