So, I promised on the main page that I would show all the places I hinted at Jim's true nature. Here we go. Remember, most of these hints were, shall we shall, almost invisible.
First Hint: Comic #161 - At this point, it's revealed the Jim's powers aren't pseudotech, psychic, or anything else that Lockdown can stop. On the other hand, Jim isn't a normal human because Lockdown didn't knock him out.
Second Hint: Comic #185 - During the alternate realities storyline, everyone who could be present in a reality bubble always was. The only one missing in this bubble was Jim. This was because the Chitrani weren't stopped on Sayleen, and thus Jim's entire species was dead in that timeline. Jim was also the one who instantly knew about how the Chitrani were defeated - it's a much bigger deal on Sayleen than on Earth, where it is just another one of the League's great accomplishments.
Third Hint Comic #195 - I still haven't decided whether Handyman actually knew that there was Christmas in Wisconsin. Probably he did, but you can call it a hint if you want.
Fourth Hint Comic #200 - Handyman knew about the Justicars. At this point, that was not as dramatically obvious, but it became clear shortly afterwards that only Magister or K'Lara could have told him those stories, the others being accounted for.
Fifth Hint Comic #201 - This would have been a heck of a lot more noticeable if we weren't in 8-bits, but Fixit's mechanics are the same shades of grey, with the same alternations, as Handyman's.
Sixth Hint Comic #240 - Jim really did have a lot of his current persona connected to that hat.
Seventh Hint Comic #244 - Also, he loves Sayleen food. And is vegetarian (well, herbivorous, technically, but you know).
Eighth Hint Comic #311 - K'Lara gives a discussion about Sayleen philosophies. Most of the things she says are a lot like what Jim says about not wanting to live in the past anymore.
General Hint: Jim's total obsession with not taking off his hat. Under any circumstance. Ever.
There were also hints dropped in the serials, but I can't find them at the moment due to my internet being slow and lazy. Suffice to say that eventually Nadia did find out that Jim was an alien, if only because eventually she was going to see him without his hat, what with them living together.