NJ numbered its turnpikes in the 1800s in order of building, between 1801 and 1850. There were eventually 72. In 1919 it started a new system, still in order of building. Some routes were duplicated, like 18. There was an 18N in the north and an 18S in the south. In the 20s they made the last big change, changing it to order of building once again. However, they also used S routes as spurs (like NJ S4 is a spur off NJ 4), and A (alt) and B (business). There were also a few N routes, like NJ 4N, which is now NJ 71, and NJ 5N, which is now NJ 53. On 1-1-1953 the Great Renumbering took place, eliminating all S routes (and the one N), and eliminating all numbers which conflicted with US route numbers, changing them to the next available number. Also, all A routes which didn't touch their parent disappeared. A little later, all routes concurrently signed with US routes (like NJ 6 with US 46) were removed. Around this time, the 1XX system started up. At first numbers were the parent + 100. But some routes couldn't do this, and they decided to start at 153 and do it in order of building. One exception was 139, which was once US 1&9 BUS, but when US 1&9 BUS was eliminated, they thought the & looked like a 3, so they numbered it 139. But NJ 139 isn't signed anyway. :-/ Also around this time (before 1941) the 2XX system started in NE NJ. There are no remnants of this - 208 is NOT one. The 5XX system replaced it. I have also seen a few 5XX routes (not the current numners) in the Frenchtown area on an old USGS topo. Some numbers also come from other states, like NJ 413 and NJ 440. Recently all ALT and BUS state routes have been eliminated, except for NJ 33 BUS in Freehold (probably because the NJ 33 freeway bypass isn't done yet). For example, NJ 47 ALT became NJ 347 (I don't know why NJ 247 wasn't used). The 2-digit numbers continue to be in order of building or numbering, with NJ 93 (?) being the most recent (NJ 94 comes from NY 94 AFAICT), unless NJ 93 came from somewhere else, in which case NJ 92 is the most recent.
Here is a list of all the NJ state routes and how each got its number (GR=Great Renumbering):

3	before the GR, except part of it was S3
4	before the GR
5	before the GR
7	before the GR
10	before the GR
12	before the GR
13	I don't know. I think it was 13E before the GR.
15	I don't know. It doesn't appear to have existed before the GR.
17	at the GR, but I don't know why. Actually, it was 17N before the 20s, so that might have something to do with it. It was 2 before the GR.
18	at the GR, but I don't know why. It was S28 before the GR.
19	I don't know. It was once 20.
20	at the GR, but I don't know why. It was 3 before the GR.
21	before the GR
23	before the GR
24	before the GR
26	before the GR
27	before the GR
28	before the GR
29	before the GR
31	after the GR, it was 30 before the GR, but became 69 at the GR but too many signs were stolen so it became 31. (I don't know why 31 was chosen)
32	after the GR, but I don't know why.
33	before the GR
34	before the GR
35	before the GR
36	before the GR
37	before the GR
38	before the GR
41	before the GR
42	before the GR
44	before the GR
45	before the GR
47	before the GR
48	before the GR
49	before the GR
50	before the GR
52	before the GR (?)
53	at the GR, was 5N (N may have been replaced by 3)
54	before the GR
55	after the GR, when it was built, but may have been proposed before the GR
56	after the GR
57	at the GR, was 24 and S24
59	at the GR, was 22
63	at the GR, was S1
64	at the GR, was 31A
66	at the GR, was S33
67	at the GR, was S1A
68	at the GR, was S39
70	at the GR, was 40
71	at the GR, was 4N
72	at the GR, was S40
73	at the GR, was S41
77	at the GR, was 46
79	at the GR, was 4 (?)
81	after the GR (?)
82	at the GR, was S24
83	at the GR, was 49
87	???
88	at the GR, was 35
90	after the GR (?)
91	after the GR (?)
93	after the GR (?)
94	came from NY (?)
109	100+9 (splits off 9)
120	100+20 (was 20)
122	100+22 (was US 22 BUS)
124	100+24 (was 24)
129	100+29 (splits off 29)
138	100+38 (was 38)
139	was US 1&9 BUS (& -> 3)
140	100+40 (splits off 40)
143	100+43 (splits off 30, which was 43, and 130 was already taken)
147	100+47 (splits off 47)
152	100+52 (splits off 52)
154	in order
156	in order
157	in order
159	in order
161	in order
162	in order
163	in order
165	in order
166	in order
167	in order
168	in order
169	in order
171	in order
172	in order
173	in order
175	in order
179	in order
181	in order
182	in order
183	in order
184	in order
185	in order
187	100+87 (splits off 87)
208	from NY 208 (was proposed to it)
284	was 84, but NY changed NY 84 to NY 284 when I-84 came along and NJ followed suit
324	was 322, I guess 324 is similar to 322, and it had to be even because it's east-west
347	300+47 (was 47 ALT)
413	from PA 413, changed at the GR from S25
439	from NY 439, changed at the GR from 28
440	from NY 440, changed at the GR from S4 and 1
444	was 4 PARKWAY, I guess they tripled the 4
445	comes after 444
446	comes after 445
495	was I-495
700	I guess they wanted a X00 and chose 700 for some reason

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