Deus Ex: Human Revolution - 360 (I believe it is the overall superior version)

Batman: Arkham City - PS3 (Exclusive DLC I believe)

Dark Souls - PS3 (Continue the series on the same system)

Dead Island - PS3 / 360 (Better graphics on PS3, better performance on 360, pick your poison)

Skyrim - 360 (Bethesda's recent games have been equal on recent platforms, but I have a feeling this one is going to favour the 360)

Dragon Age - PS3 / 360 (Same as Dead Island)

Battlefield 3 - PS3 (Advantage in graphics and installation size)

Some of them have obvious advantages, others are just suited to the systems.

DeUS eX:Human Revolution : 360 version.

Batman: Arkham City : PS3. I believe its the same across both platforms, the controller will be better I guess.

Dark Souls : PS3. Will have better audience who is experienced this series already.

Dead Island : 360. Heard the PS3 version has problems.....

Skyrim : I think this will be good on both the systems...but since this isn't out for some time its ok, I don't really know.

Dragon Age :

DON'T get it on the PS3. Seriously no. You will regret it and it is the most inferior version. That is if you are talking about the origins. If you are talking about the second one then you should get the PS3 version.

Battlefield3 : PS3 version. 360 if friends are buying it or controller preference.

This.

Did you get any of the earlier games in those series (Demon Souls, Arkham Asylum) yet? Get the sequels for the same system. You don't want to break up the set.

If you care about your Gamerscore, since it seems like you do with you mentioning it, I would get them all for the 360. And just get the exclusives for your PS3. I basically do the same thing just switched around. Trophies meean more to me, and I get everything on the PS3, get exclusives for 360.

Dark Souls just same

they both have frame-rate problem

http://www.eurogamer.net/articles/digitalfoundry-dark-souls-face-off

of course,for more people playing,should still choose PS3 version

Based on Lens of Truth:

Deus Ex: Human Revolution: Tie
Batman: Arkham City: 360
Dark Souls: Tie
Dead Island: Tie
Dragon Age: PS3
Battlefield 3: PS3

Deus Ex: Personal preference (the controller you like better)
Batman: Read Above
Dark Souls: Equal, but PS3 should have better online experience considering there are more players on there.
Dead Island: 360, more players online and i heard the game had screen tearing on PS3, i have only played the PC version so don't take this as hard fact.
Dragon Age: Only played the 360 version, worse graphics from what i heard, but better frame rates or loading time cant say. The PC version is a lot better though, but if you must get console: i would say personal preference, loading times or graphics?
Skyrim, not out, probably 360 though, considering Oblivion, Fallout 3 and New Vegas.
Battlefield probably PS3 you get extra content right? Online base will be huge on both, so it comes down to the controller imo, if the extra content is bad.

Take your friends into consideration though (where you know your friends will play with you) and your preferred controller. I got all these games for PC except Batman which i got for Xbox because i generally play all multi platforms on that, since i had it first and back in the day they all used to be better. The exceptions like FFXIII etc i got for PS3 though, but PC is my main platform so i get most games for that.

Deus Ex: Definitely 360. Much better lighting and vibrant colours
Batman: As far as I can tell, no major differences.
Dark Souls: PS3
Dead Island: PS3 has better graphics but inconsistent framerate, 360 looks worse but has more stable framerate. Take your pick.
Skyrim: Dunno, it's not out yet.
Dragon Age: Same with Dead Island. PC is recommended.
Battlefield 3: PS3 if you have to choose between the two, but I recommend PC more than either of those.

Batman: Arkham City PS3 = Joker

Dark Souls PS3.