This article includes a list of Scottish Gaelic words of possible non-Indo-European origin. (In progress). This article will likely contain fewer words than originally planned and only some of the possible pre IE words I have found. Note that this article was originally titled: 27: General non-IE Gaelic vocabulary, (long article, being updated). Note that this section does not include a large number of or even many of the Gaelic cognates I have published about on the ebooks available on this site and in other books.

1). Giogh- as in the island names Giogha and Gioghaigh - possibly related to Icelandic gjá and Gaelic geodha and Manx ghaw in place-names, and Orkney Scots geo, but this does not quite make sense I think as there are not that many "geos" on either island, so instead I wonder if these island names connect to a female goddess entity, in which case there might be a connection with the word Sheela-na-Gig, where the "Gig" element is not fully understood etymologically, but where there is an obvious connection to female goddess figures. I also think that the root word present in these words could be connected to Icelandic gýgr referring to a giantess, compare also Orkney Norn: gýro and Norwegian gyger. 

2). athach - "giant" or "monster". This word can also mean "a peasant" however. The word athach can also mean a gust of wind, which is interesting.
3). Fadhail - "ford", lends its name to the island of Benbecula, related to Germanic and Latin words and to English "wade", but likely I think of non-Indo-European origin.
4). oro- as in the names Oronsay and Orosay, perhaps connected to Uralic *ura - groove or channel, which may make sense given the way that both Oronsay and Orosay and separated from the mainland by shallow channels. 

5). ciuthach - another form of giant or aquatic ancestor. Related to Manx Cughtagh. I have written about these ancestors quite a lot before, because there are some really interesting things pertaining to them and to the prehistoric peoples of Western Scotland. I would like to mention in this article specifically though something pertaining to them and the folklore of Yorkshire.

8). giosagach - magical, unknown etymology

12). pruchlais - den or cave, according to Am Faclair Beag ( faclair.com ). This word is likely related to brugh - "broch", although the formation of the word pruchlais may imply other information coded into the word's syllables. 

14). ròig - den or cave, according to Am Faclair Beag ( faclair.com ). Unknown etymology. Possibly related to Finnish rotko - "chasm", "ravine" or "gully". 

16). sgailp - den or cave, according to Am Faclair Beag ( faclair.com ). Unknown etymology. Perhaps connected to Orkney Scots gloup for a geo-like coastal feature, and perhaps related to English "gulp" as in to swallow.  

17). cuta - a short log (2)

(2): A pronouncing and etymological dictionary of the Gaelic language, by Malcomb MacLennan