For Pathfinder, as mentioned in the comments above, Crossbow Mastery is pretty useful. Otherwise, as far as feats go, you've got 'em covered.
The Far Shot feat will turn the -2 range increment penalties into -1, which can be very useful to shoot from long range.
Here's where some cheese comes in-- when you take a 1-level dip in Rogue with the Sniper Archetype, you gain the Accuracy ability, which that further by half. This does stack RAW, which effectively doubles your range increment distance before you even see a penalty. For example, you can pick stuff off from almost half a mile away with only a -4 penalty. Granted, you'd need scrying or something to spot your targets, but your stealth check gets hilarious... Your GM will probably scowl at you for this. Pay him back by taking Leadership and Siege Engine feats... and chuck donkeys at the BBEG from the next county. On a more serious note, the Ballista is good and can be used every turn like this.
If your GM allows material from 3.5e, then you can take both Crossbow Sniper and Improved Crossbow Sniper. The former grants you half your Dex modifier to damage and a +30 feet to Sneak Attack and Skirmish ranges, and the latter bumps it up to full dex and an additional 30 feet. Furthermore, a 1-level dip in Rogue grants you a Sneak Attack, and the Craven feat from 3.5 will grant you your character level as bonus damage to SAs (at the cost of -2 will saves against fear effects).
If your GM will allow things from 3.0, you can attach a Gnome Crossbow Sight to your xbows to ignore the first two range increment penalties.
As a GM, I allow pretty much all things regarding crossbows in Pathfinder, because they're already such a sub-optimal weapon compared to bows, thanks to the absence of the strength modifier to damage and manyshot. You'll probably be using the Launching Crossbow as an Alchemist, so your experience won't be as bad as most classes, but the feat tax for using any crossbow is almost ridiculously heavy.
A little bit more cheese, but if you take a 1-level dip in Oracle, choose the Waves mystery, and take Water Sight as your first-level revelation, you'll be able to lay down Obscuring Mist a few times a day and be able to see through it without penalty. Being able to shoot with guaranteed total concealment is a huge plus to tactical fighting (its the basis for my Sniper using crossbows in my current PF game, in fact, since the concealment guarantees Sneak Attacks)
By RAW there is no way to answer this for sure, magic missile does say it generates multiple missiles but this seems to be flavour rather than mechanical.
The key part I'm relying on in this answer is in the description of toppling spell:
your force spell [snip] If the target takes damage
This clearly says that if the spell deals damage to the target then you get a trip attempt. It does not say anything about damaging the target multiple times, it just says that if the spell deals damage.
Based on this part of the rules the way I've been using the spell is to say that you get a trip attempt against each target struck by the spell that you deal damage to no matter how many missiles you hit that target with. If you hit three targets you get three trip attempts (one on each). If you hit one target three times you get a single trip attempt.
I'm aware of the sneak attack/rays FAQ but it's speaking about a completely different ability and a completely different style of spell so I do not see how it applies.
Low-level wizards measure up fine because…
Low-level combats are incredibly lethal
In a group of brand new, fresh-from-the-core-rules group of PCs, the wizard—with his bad Armor Class, bad weapon proficiencies, low hp, middlin' class features, and 2 or 3 spells per day—will appear to be unable to measure up to the killin'-all-the-time fighter or the I've-spells-and-armor-and-weapons-and-channeling cleric.
But, then, look at this orc. He has AC 13 and 6 hp, but he's attacking at +5 to hit for 2d4+4. His ferocity extraordinary ability gives him sort of, like, 10 extra hp, and that falchion—with its wide threat range—makes a lot of level 1 characters just dead.
There're 3 of those orcs in an EL 1 encounter.
And you can expect 4 encounters each day.
There's a lot of adventurer blood on those falchions, and it's not all wizard blood… although it may feel that way sometimes.
Beginning wizards use crossbows
Most folks who sign up to play wizards think they're going to get to play Raistlin, Gandalf, or Harry Potter, but then, after winning the the day's first and second encounters via the spells color spray or sleep, those beginning wizards are out of spells and stuck with their light crossbows.
You know what that makes them? Crossbowmen. A beginning wizard without spells should act like an archer because he is. An archer stays in the back. An archer delays and readies until he's got a clear shot. An archer lets his party know if someone needs to move. An archer moves if he can't get a clear shot. An archer spends some of his treasure on archery stuff—masterwork bolts just aren't that expensive, and a dozen is probably enough. An archer uses cover. A crossbowman can even drop prone to avoid enemy missile fire and keep firing. Seriously, a beginning wizard can apply his arcane bond class feature to a light crossbow and just start with a masterwork one:
Such a wizard will take crap from theoretical optimizers, but, y'know, it doesn't matter how awesome a character would've been if he's dead.
Low-level combats are supposed to teach everybody how combat—mundane and magical—will be run with that GM in that campaign, and all players and characters need to be on the same page for when they engage in bigger combats with nastier threats later.
A sample shopping list
A starting wizard has an average of 70 gp. Here's a possible shopping list:
Rolling well on starting wealth adds to this list the following:
With this load, the starting wizard casts his 2 to 4 spells per day then dons leather armor and becomes a crossbowman. The wizard should even rest in that leather armor, too, if he's cast all his spells for the day anyway.
It's understandable that most wizards don't want to be crossbowmen. Here're some ways out of that bind.
Patient wizards contribute more and live longer
Having a beginning wizard in the party is a burden. He needs his beauty sleep to prepare spells. He's got a really wide but very shallow power meter. After one or maybe two encounters the wizard should encourage the party to knock off for the day, reminding the party that—despite their impatience—it's better to have their wizard at full power than have just another crossbowman.
Encourage the GM to start the campaign at a level greater than 1
This might be the real problem. Some GMs never get the idea that campaigns can start at any level the GM wants. Really, there are very, very few pieces of media that simulate a character's growth from Wizard Who Casts Sleep Once Per Day to Wizard Who Casts Wish Thrice Per Day, and, really, most folks want to play something in between anyway. Talk to the GM. See if the GM'd be willing to start a campaign at level 3 or 6 or 10 or whatever instead of always 1. Or start such a campaign yourself—then your bad guys are casting at the PCs the awesome spells you've always wanted your characters to cast (and now those are your characters!), and when those bad guys are defeated, you get to try different bad guys with different spells versus the PCs.