Bending up flathead screwdrivers can come in handy - I've got a couple that are "purpose-bent." One for servicing a front end on a 1990-ish Nissan Sentra (didn't want to drop the final drive into the transaxle case while changing halfshafts,) and a 1/4"x8" cabinet flattie with the last 1/4" bent into a slight reverse hook for a tappet grabber.
Got a bridge puller kit I made for pulling an AW4 apart, and a pair of "large snapring chopsticks" I made by taking 1/4" aluminum rod stock and drilling/tapping the end with a #4-40 hole, and then putting in a #4-40 headless setscrew. Call those two about $20 worth of stock and screws to save whatever the "special puller kit" would have cost me - something like $200-$250 bones, I'm sure (and this was a good ten years ago...)
Large wooden blocks can come in handy. Use a 1-1/4" and a 3/8" Forstner bit to drill holes to keep the valvetrain sorted while you're working, make sure to mark one end as FRONT. One row of 1-1/4" holes to hold the tappets, one row of 3/8" holes to hold the pushrods, and another to keep the rockers/pivots/bridges/screws sorted. (Even if you don't plan to reuse the parts, you still want to keep them sorted for inspection. If the block is large enough, a series of 5/8" holes will also serve to retain spark plugs in order - you'll probably want something like a 4"x8" or so to make this work.) Use hardwood, soak with clean engine oil (varnish/paint can flake off onto parts.)
Foot-long bits of rubber or vinyl hose make for good screw guides - whether you're trying to keep from dinging up your crankshaft or just getting things together.
Keep your old pushrods - they usually make handy alignment pins for fabrication and assembly work. A bit of black heatshrink to show that they're tools and not parts won't go amiss ("blacklining" is the standard method I use for decommissioning anything. A climbing rope that has been retired to utility use will be cut to length, burned to seal, and an inch or so of black POHST will be applied to each end to show its status. Ditto toothbrushes that get transferred to the toolbox - I don't want them to get mixed up with anything I actually use on my teeth before I managed to get them all greasy. You get the idea.) Keeping assorted sizes of threaded rod about will give you more flexibility for similar results - you probably won't need any one piece longer than a foot. I try to keep SAE around up to 1/2" UNC and UNF, and ISO up to M10-1.5 (also comes in really handy for fabbing up tools, pullers, pushers, and the like in a pinch.)
I'm going to have to write up a list of "shop tips" one of these days, aren't I? Most of the stuff may not fall under AdFab, but I'm sure most of it will be useful to someone-or-other...
Old tappet casings come in handy for screw-ram pressor feet, and the slight crown usually results in not marring or gouging the sheetmetal. Pull the snapring and plunger, you can use a nut and washer to bear against the snapring on reassembly (or the snapring itself) to retain the tappet casting to whatever you're using as a jackscrew.
Keep checking around, and you'll manage to find a tool that is somewhat like narrow duckbill pliers turned inside-out (the jaws move apart when the handles are squeezed.) I picked up a pair of these somewhere twenty-odd years ago, and I use them all over the place! I no longer have any idea where I got them, why I got them, or how much I got them for; but they're handy!
Got a junk box full of screws? MSC Direct has a wifty little tool called a "Thread Detective" - SAE and ISO common threads to 1/2" (SAE) or M12 (ISO.) Worth the bux - about twenty-five of them, I think - to get that mess finally sorted once and for all! Not a direct fab tool, but it comes in really handy. It's a series of inside/outside threaded aluminum bungs on a cable with an eye/loop crimped into each end for easy hanging. Easier to work with than leaf gages and a caliper/mike/rule...
A good, strong, small flashlight is a good tool for checking for clearance in between parts before/after assembly. I favour the Surefire G2Z for this. It will go anywhere your hand will fit, and it has the Maglites beat all hollow for brightness. Check for gaps between sheetmetal, mill stock, castings, whatever - you can also use a bright light with a well-focused beam for checking for variations in the surface of a sheetmetal part or a large plate/bar by shining the lamp across the surface and looking for shadowed areas (old body shop trick - that and spraying a "guide coat" of primer before a final sanding. High spots will strip first.)
Working with a bunch of fasteners, and you want to keep them handy and NOT rolling about? Wrap a layer of duct tape about your forearm - sticky side out - and use that to keep your screws/nuts/rivets/whatever handy. Works especially well for Nylon, rubber, or aluminum bits that don't stick to magnets...