clusters = [
            [[1, 1], [1, 2]],
            [[0, 2], [1, 1]],
            [[1, 2], [2, 1]], 
[[3, 2], [3, 0]], [[0, 4], [1, 3]], [[2, 4], [3, 5]], [[4, 5], [4, 3]], [[2, 7], [2, 5]], [[0, 8], [0, 6]], [[1, 8], [1, 6]], [[2, 8], [2, 6]], [[3, 8], [3, 6]]
]

clusters = [[[1, 1], [1, 2]], [[0, 2], [1, 1]], [[1, 2], [2, 1]],
            [[3, 2], [3, 0]], [[0, 4], [1, 3]], [[2, 4], [3, 5]],
            [[4, 5], [4, 3]], [[2, 7], [2, 5]], [[0, 8], [0, 6]],
            [[1, 8], [1, 6]], [[2, 8], [2, 6]], [[3, 8], [3, 6]], ]

def cluster_filter(cluster):
    a, b = cluster
    return len(set(a) & set(b))

print filter(cluster_filter, clusters)

[
[[1, 1], [1, 2]], [[1, 2], [2, 1]], [[3, 2], [3, 0]], 
[[4, 5], [4, 3]], [[2, 7], [2, 5]], [[0, 8], [0, 6]], 
[[1, 8], [1, 6]], [[2, 8], [2, 6]], [[3, 8], [3, 6]]
]

[
 [  [[1, 1], [1, 2]],
    [[0, 2], [1, 1]],
    [[1, 2], [2, 1]] ], 
# связующие элементы [1,1] и [1,2] 
 [  [[...], [...]],
    [[...], [...]],
    [[...], [...]] ]
]

def cluster_grouper(clusters):
    grouped = []
    result = []

    for cls in clusters:
        if cls in grouped:
            continue
        grouped.append(cls)
        groups = [cls,]
        a, b = cls
        for ccls in clusters:
            if (ccls not in grouped) and (a in ccls or b in ccls):
                grouped.append(ccls)
                groups.append(ccls)
        result.append(groups)
    return result