I compared a complete 1988 Donruss Factory set to around 3,000 cards I acquired via packs - card by card - and was able to determine that there are 319 different border variations.
While all six checklists have text variations on them, five of them (#'s 100, 300, 400, 500, 600) also have border variations, bringing up the total to 324.
Here are the 319 cards that have border variations (excluding the checklist variations listed above):
3, 6, 9, 11, 13, 15, 17, 21, 23, 24, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 49, 50, 51, 52, 53, 54, 55, 57, 58, 59, 60, 61, 62, 63, 72, 80, 81, 82, 83, 84, 85, 86, 87, 96, 97, 98, 99, 101, 102, 103, 110, 119, 124, 125, 126, 135, 136, 137, 138, 139, 140, 141, 142, 150, 159, 160, 161, 166, 167, 168, 169, 170, 171, 172, 173, 180, 181, 190, 191, 192, 193, 194, 195, 198, 199, 206, 207, 208, 209, 210, 211, 212, 213, 221, 222, 223, 229, 230, 231, 232, 237, 238, 239, 240, 241, 242, 245, 246, 253, 254, 255, 256, 257, 258, 259, 260, 269, 270, 271, 272, 276, 277, 278, 279, 280, 281, 282, 283, 285, 286, 287, 288, 289, 290, 291, 304, 305, 306, 307, 316, 317, 318, 319, 324, 325, 326, 327, 328, 329, 330, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 356, 357, 358, 359, 360, 361, 362, 366, 367, 368, 369, 371, 372, 373, 374, 375, 376, 377, 378, 386, 387, 388, 389, 390, 391, 392, 393, 396, 397, 398, 399, 402, 403, 404, 405, 406, 407, 408, 410, 411, 412, 413, 414, 415, 416, 417, 426, 434, 435, 436, 437, 438, 439, 440, 443, 444, 445, 446, 447, 448, 457, 458, 459, 460, 461, 462, 463, 464, 470, 471, 472, 479, 480, 493, 494, 495, 501, 502, 503, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 532, 533, 534, 535, 544, 545, 546, 547, 548, 549, 551, 552, 553, 554, 555, 556, 557, 558, 566, 575, 576, 577, 578, 579, 580, 581, 582, 591, 592, 599, 603, 604, 605, 608, 609, 613, 617, 622, 623, 624, 626, 627, 629, 632, 633, 638, 639, 640, 642, 643, 646, 647, 649, 651, 655, 656, 657, 658