I don't think Southerness gets many mentions on GCA, but there are several excellent holes, especially the 3rd, 5th and 12th, though there are no weak holes.
Nairn is rarely mentioned but I think the 3rd and 4th, 8th, 13th, 14th and 15th are particularly fine.
Seacroft is generally off the GCA radar but there are some corkers such as the 4th, 5th, 7th, and the outstanding 13th.
Hunstanton is infrequently cited and the 6th, 7th, 11th, 13th, 14th (yes, despite its being a totally blind par 3!), 16th, 17th and 18th are very fine holes.
Aldeburgh is a personal favourite with the 4th-7th a great sequence of holes, the 10th, 11th and 15th also outstanding.
Crowborough Beacon has a number of terrific holes, most notably the 2nd and 6th and the diminutive 13th.
I should bringing up the subject of bunkerless Berkhamstead, but I can't really say that there are any truly outstanding holes, more that the overall challenge is considerable.
I certainly agree with Tom Doak about the merits of Halifax which has exceptional par 4s at the 3rd, 4th and 5th, a mad 258-yard blind par 4 at the 12th and a stunning drop shot down a mountainside at the 17th.
Brancepeth Castle has many exciting holes played across ravines, with the short, par-4 8th followed by terrific back-to-back par 3s and many another fine hole.
Sandiway (Ray/Colt) is not a total architecural gem, but there are some very fine holes, particularly the immensely strong par 4s at the 10th, 12th and 14th. I like its opening hole, too, and the 17th is a good short par 4.
Seascale raises the spirits, with the 3rd, 9th, 13th, 14th, 15th and 17th worth the visit, and poweful players might also like the 16th, but it is too hard for me!
In Wales most players try to make it to nefyn, for the fabulous views and the eccentricity of the back nine, but I should love to alert the curious to Porthmadog. It is not a great course, and it is not entirely links, but the back nine most certainly is links golf of the best kind, and the sequence from the 11th to the 15th is marvellous.
Another Welsh minor masterpiece is Holywell, wild and woolly, like the sheep which roam the course freely. True, there are a few weak holes early in the round, but the course steps up several gears when you cross the road on the 11th. From here to the 17th there are some cracking holes with the short 12th, par-5 14th, short 15th and the 333-yard 17th marvellous fun - the green on the 17th being particularly wickedly attended by grassy hollows and devious contours.
Tom Williamsen did a lovely write up of Cavendish on this site and it certainly has a number of outstanding holes, the 5th, 8th, 9th, 10th, 11th and 18th being the most distinguished.
Don't forget Prestbury, either, with an excellent opening hole, the short 7th, monstrous 9th, demanding 13th, and superb 16th perhaps the finest holes on a course with few weaknesses.
I'll also put in a word for Hamburger-Falkenstein, with my favourite holes being the 5th, 6th, 7th, 13th, 14th and 17th.