In cloackwood when that spider thingy talks it says that it was made this way by Jon Icarus and then also mentions something about his wife... Is that reference to Jon Irenicus and Ellesime?

Also is the face sculpture that Prism made that of Ellesime?

Prism does indeed sculpt Ellisime, but the Icarus reference is fuzzy. Bioware intended to hint at BG2 with Jon Icarus, but the designers felt the name was too Greek, so they changed it to Irenicus. (There's also a hint about Neverwinter Nights in the Nashkel carnival.)

There are multiple BG2 references in BG1. Jon Icarus is one of the easier ones to find.

Spoiler (BG2)
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I havent played BG1 after BG2 so cant really remember any references... I just wonder, is there anything in BG1 to hint that Imoen is your sister?

Response to BG2 spoiler....
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Other than the fact that you are of comparable ages, the two of you have been taken to Candlekeep together... There's things to make you perhaps suspect, but nothing really tangible in there.

One of the most superb hints is Lord Foreshadow, some guy you meet on the road - depending on the dialogue choice you choose, he either tells you that Neverwinter is soon to become a very popular holiday destination, or that things are brewing in Athkatla.

I enjoy that you can tell him that it sounds preposterous and doubt such a place exists. He just says...
"Not yet, but soon."

This is a BG2 SPOILER AS WELL:

One of the options as a password to enter the shadow thieves' guild is 'Bodi,' which probably refers to the vampiress Bodhi from BG2.

The seer Pallonia has some interesting things to say:
<font color=green>Well, just across the southern mountains there are troubles brewing in great Amn that will make our current concerns seem small by comparison. To the far north there is a city where winter never rears its ugly head; a city that has not been seen nor heard from for many a year, but will soon welcome the return of a multitude of citizens. Both of these events will unfold regardless of our current troubles. Great may be our concerns, but much more is on the horizon. Leave me be, I have much to think upon.</font>

This is a BG2 SPOILER AS WELL:

One of the options as a password to enter the shadow thieves' guild is 'Bodi,' which probably refers to the vampiress Bodhi from BG2. </font>[/QUOTE]Oh, if we're playing the name game, then... {ToB spoiler}
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You encounter a lady named Sendai in... The Cloudpeaks, is it? Some southern area... Anyway, she makes a 'joke' that had something to do with hunting you for sport. Very much like your sister in ToB... except not nearly as shrill.